This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.\".
\nDescription: This dataset consists of raw sequencing snATAC-seq data (10x Genomics Chromium Next GEM Single Cell ATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n\n\n", + "access_right": "open", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "version": "0.1", + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ], + "license": "cc-by-4.0", + "imprint_publisher": "Zenodo", + "upload_type": "dataset", + "prereserve_doi": { + "doi": "10.5281/zenodo.18988730", + "recid": 18988730 + } + }, + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.", + "links": { + "self": "https://zenodo.org/api/records/18988730", + "html": "https://zenodo.org/records/18988730", + "doi": "https://doi.org/10.5281/zenodo.18988730", + "parent_doi": "https://doi.org/10.5281/zenodo.18988729", + "badge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988730.svg", + "conceptbadge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988729.svg", + "files": "https://zenodo.org/api/records/18988730/files", + "bucket": "https://zenodo.org/api/files/178391d7-e533-4931-9972-c555e853c6ad", + "thumb250": "https://zenodo.org/record/18988730/thumb250", + "thumbs": { + "10": "https://zenodo.org/record/18988730/thumb10", + "50": "https://zenodo.org/record/18988730/thumb50", + "100": "https://zenodo.org/record/18988730/thumb100", + "250": "https://zenodo.org/record/18988730/thumb250", + "750": "https://zenodo.org/record/18988730/thumb750", + "1200": "https://zenodo.org/record/18988730/thumb1200" + }, + "latest_draft": 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"https://zenodo.org/api/records/18988730/files/0d6da991-092e-4c1b-8cce-71ec2860f7d4", + "download": "https://zenodo.org/api/records/18988730/draft/files/voet-pmdbs-sn-atacseq-10x_README.pdf/content" + } + } + ], + "state": "done", + "submitted": true +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/dataset.doi b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/dataset.doi new file mode 100644 index 0000000..fb119f0 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/dataset.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988729 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/project.json b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/project.json new file mode 100644 index 0000000..9ecf4c6 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/project.json @@ -0,0 +1,56 @@ +{ + "project_name": "Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource", + "project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.", + "dataset_description": "This dataset consists of raw sequencing snATAC-seq data (10x Genomics Chromium Next GEM Single Cell ATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium\nLaboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium\nDepartment of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium\nKU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "30-09-2025", + "version": "1.0", + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/version.doi b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/version.doi new file mode 100644 index 0000000..f6cc2f4 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988730 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x.json b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x.json new file mode 100644 index 0000000..a3ebbe7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.\".
\nDescription: This dataset consists of raw sequencing snATAC-seq data (10x Genomics Chromium Next GEM Single Cell ATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "30-09-2025", + "version": "1.0", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium\nLaboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium\nDepartment of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium\nKU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.md b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.md new file mode 100644 index 0000000..6ec13c2 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.md @@ -0,0 +1,64 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – 10x snATAC-seq.". + +## Dataset Description: + +This dataset consists of raw sequencing snATAC-seq data (10x Genomics Chromium Next GEM Single Cell ATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium +Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium +KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-atacseq-10x, v1.0 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 30-09-2025 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.pdf b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.pdf new file mode 100644 index 0000000..43fb624 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-10x/DOI/voet-pmdbs-sn-atacseq-10x_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/refs/Voet_pmdbs_sn_atacseq_10x_Dataset_Information.docx b/WIP/voet-pmdbs-sn-atacseq-10x/refs/Voet_pmdbs_sn_atacseq_10x_Dataset_Information.docx new file mode 100644 index 0000000..5e727c1 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-10x/refs/Voet_pmdbs_sn_atacseq_10x_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-atacseq-10x/version b/WIP/voet-pmdbs-sn-atacseq-10x/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-10x/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/10.5281_zenodo.18988735 b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/10.5281_zenodo.18988735 new file mode 100644 index 0000000..fe4ecf1 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/10.5281_zenodo.18988735 @@ -0,0 +1,2 @@ +ALL_VERSIONS : https://doi.org/10.5281/zenodo.18988735 +CURRENT : https://doi.org/10.5281/zenodo.18988736 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/beta-deposition.json b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/beta-deposition.json new file mode 100644 index 0000000..05833c2 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/beta-deposition.json @@ -0,0 +1,116 @@ +{ + "created": "2026-03-12T19:16:25.464575+00:00", + "modified": "2026-03-12T19:16:26.042330+00:00", + "id": 18988736, + "conceptrecid": "18988735", + "doi": "10.5281/zenodo.18988736", + "conceptdoi": "10.5281/zenodo.18988735", + "doi_url": "https://doi.org/10.5281/zenodo.18988736", + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.", + "doi": "10.5281/zenodo.18988736", + "publication_date": "2026-03-12", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.\".
\nDescription: This dataset consists of raw sequencing snATAC-seq data (HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n\n\n", + "access_right": "open", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "version": "0.1", + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ], + "license": "cc-by-4.0", + "imprint_publisher": "Zenodo", + "upload_type": "dataset", + "prereserve_doi": { + "doi": "10.5281/zenodo.18988736", + "recid": 18988736 + } + }, + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.", + "links": { + "self": "https://zenodo.org/api/records/18988736", + "html": "https://zenodo.org/records/18988736", + "doi": "https://doi.org/10.5281/zenodo.18988736", + "parent_doi": "https://doi.org/10.5281/zenodo.18988735", + "badge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988736.svg", + "conceptbadge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988735.svg", + "files": "https://zenodo.org/api/records/18988736/files", + "bucket": "https://zenodo.org/api/files/86a0b798-fe4b-42ed-9f74-30bce31b3941", + "thumb250": "https://zenodo.org/record/18988736/thumb250", + "thumbs": { + "10": "https://zenodo.org/record/18988736/thumb10", + "50": "https://zenodo.org/record/18988736/thumb50", + "100": "https://zenodo.org/record/18988736/thumb100", + "250": "https://zenodo.org/record/18988736/thumb250", + "750": "https://zenodo.org/record/18988736/thumb750", + "1200": "https://zenodo.org/record/18988736/thumb1200" + }, + "latest_draft": 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"project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.", + "dataset_description": "This dataset consists of raw sequencing snATAC-seq data (HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "2026-03-12", + "version": "0.1", + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/version.doi b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/version.doi new file mode 100644 index 0000000..229bebc --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988736 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop.json b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop.json new file mode 100644 index 0000000..46fdcd0 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 HyDrop-ATAC v2.\".
\nDescription: This dataset consists of raw sequencing snATAC-seq data (HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "2026-03-12", + "version": "0.1", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.md b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.md new file mode 100644 index 0000000..240d7d6 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.md @@ -0,0 +1,49 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – HyDrop-ATAC v2.". + +## Dataset Description: + +This dataset consists of raw sequencing snATAC-seq data (HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-atacseq-hydrop, v0.1 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 2026-03-12 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.pdf b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.pdf new file mode 100644 index 0000000..7798ba5 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-hydrop/DOI/voet-pmdbs-sn-atacseq-hydrop_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/refs/Voet_pmdbs_sn_atacseq_hydrop_Dataset_Information.docx b/WIP/voet-pmdbs-sn-atacseq-hydrop/refs/Voet_pmdbs_sn_atacseq_hydrop_Dataset_Information.docx new file mode 100644 index 0000000..343dfe4 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-hydrop/refs/Voet_pmdbs_sn_atacseq_hydrop_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-atacseq-hydrop/version b/WIP/voet-pmdbs-sn-atacseq-hydrop/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-hydrop/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/10.5281_zenodo.18988717 b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/10.5281_zenodo.18988717 new file mode 100644 index 0000000..e5bd7c7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/10.5281_zenodo.18988717 @@ -0,0 +1,2 @@ +ALL_VERSIONS : https://doi.org/10.5281/zenodo.18988717 +CURRENT : https://doi.org/10.5281/zenodo.18988718 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/beta-deposition.json b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/beta-deposition.json new file mode 100644 index 0000000..78bce67 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/beta-deposition.json @@ -0,0 +1,116 @@ +{ + "created": "2026-03-12T19:16:05.502764+00:00", + "modified": "2026-03-12T19:16:06.410673+00:00", + "id": 18988718, + "conceptrecid": "18988717", + "doi": "10.5281/zenodo.18988718", + "conceptdoi": "10.5281/zenodo.18988717", + "doi_url": "https://doi.org/10.5281/zenodo.18988718", + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.", + "doi": "10.5281/zenodo.18988718", + "publication_date": "2026-03-12", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.\".
\nDescription: This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC pre-indexing followed by 10x Genomics snATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1, https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000496_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v2_UserGuide_RevB.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
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analyses: a unique data resource", + "project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.", + "dataset_description": "This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC pre-indexing followed by 10x Genomics snATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1, https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000496_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v2_UserGuide_RevB.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "2026-03-12", + "version": "0.1", + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/version.doi b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/version.doi new file mode 100644 index 0000000..3d417ba --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988718 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x.json b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x.json new file mode 100644 index 0000000..fed423c --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + 10x Genomics.\".
\nDescription: This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC pre-indexing followed by 10x Genomics snATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1, https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000496_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v2_UserGuide_RevB.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "2026-03-12", + "version": "0.1", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.md b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.md new file mode 100644 index 0000000..f6a628f --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.md @@ -0,0 +1,49 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – Scale-ATAC + 10x Genomics.". + +## Dataset Description: + +This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC pre-indexing followed by 10x Genomics snATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1, https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000496_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v2_UserGuide_RevB.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-atacseq-scalebio-10x, v0.1 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 2026-03-12 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.pdf b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.pdf new file mode 100644 index 0000000..2b05b63 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/DOI/voet-pmdbs-sn-atacseq-scalebio-10x_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/refs/Voet_pmdbs_sn_atacseq_scalebio_10x_Dataset_Information.docx b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/refs/Voet_pmdbs_sn_atacseq_scalebio_10x_Dataset_Information.docx new file mode 100644 index 0000000..e0e8c61 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/refs/Voet_pmdbs_sn_atacseq_scalebio_10x_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/version b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-10x/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/10.5281_zenodo.18988743 b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/10.5281_zenodo.18988743 new file mode 100644 index 0000000..7757e5c --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/10.5281_zenodo.18988743 @@ -0,0 +1,2 @@ +ALL_VERSIONS : https://doi.org/10.5281/zenodo.18988743 +CURRENT : https://doi.org/10.5281/zenodo.18988744 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/beta-deposition.json b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/beta-deposition.json new file mode 100644 index 0000000..fdbc763 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/beta-deposition.json @@ -0,0 +1,116 @@ +{ + "created": "2026-03-12T19:16:35.111591+00:00", + "modified": "2026-03-12T19:16:35.788717+00:00", + "id": 18988744, + "conceptrecid": "18988743", + "doi": "10.5281/zenodo.18988744", + "conceptdoi": "10.5281/zenodo.18988743", + "doi_url": "https://doi.org/10.5281/zenodo.18988744", + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.", + "doi": "10.5281/zenodo.18988744", + "publication_date": "2026-03-12", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.\".
\nDescription: This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC + HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing libarary. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n\n\n", + "access_right": "open", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "version": "0.1", + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ], + "license": "cc-by-4.0", + "imprint_publisher": "Zenodo", + "upload_type": "dataset", + "prereserve_doi": { + "doi": "10.5281/zenodo.18988744", + "recid": 18988744 + } + }, + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's 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single-cell multi-omics analyses: a unique data resource", + "project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.", + "dataset_description": "This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC + HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing libarary. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "2026-03-12", + "version": "0.1", + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/version.doi b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/version.doi new file mode 100644 index 0000000..1dfbb75 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988744 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop.json b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop.json new file mode 100644 index 0000000..31ce063 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 Scale-ATAC + HyDrop v2.\".
\nDescription: This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC + HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing libarary. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "2026-03-12", + "version": "0.1", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.md b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.md new file mode 100644 index 0000000..466813d --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.md @@ -0,0 +1,49 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – Scale-ATAC + HyDrop v2.". + +## Dataset Description: + +This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC + HyDrop v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.x54v97mmpg3e/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing libarary. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-atacseq-scalebio-hydrop, v0.1 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 2026-03-12 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.pdf b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.pdf new file mode 100644 index 0000000..e72370b Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/DOI/voet-pmdbs-sn-atacseq-scalebio-hydrop_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/refs/Voet_pmdbs_sn_atacseq_scalebio_hydrop_Dataset_Information.docx b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/refs/Voet_pmdbs_sn_atacseq_scalebio_hydrop_Dataset_Information.docx new file mode 100644 index 0000000..733d665 Binary files /dev/null and b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/refs/Voet_pmdbs_sn_atacseq_scalebio_hydrop_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/version b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-atacseq-scalebio-hydrop/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/dataset.doi b/WIP/voet-pmdbs-sn-multimodal/DOI/dataset.doi new file mode 100644 index 0000000..7c6b57d --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/DOI/dataset.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988753 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/project.json b/WIP/voet-pmdbs-sn-multimodal/DOI/project.json new file mode 100644 index 0000000..2a92143 --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/DOI/project.json @@ -0,0 +1,56 @@ +{ + "project_name": "Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource", + "project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x multiome (snRNA-seq and snATAC-seq).", + "dataset_description": "This dataset consists of raw sequencing snRNA-seq data and snATAC-seq data (10x Genomics Chromium Next GEM Multiome ATAC/GEX). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-and-permeabilisation-of-fresh-fro-n2bvj3yqnlk5/v1, https://cdn.10xgenomics.com/image/upload/v1728078404/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdf.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium\nLaboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium\nDepartment of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium\nKU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "30-09-2025", + "version": "1.0", + "title": "Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x multiome (snRNA-seq and snATAC-seq).", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/version.doi b/WIP/voet-pmdbs-sn-multimodal/DOI/version.doi new file mode 100644 index 0000000..d99b256 --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988754 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal.json b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal.json new file mode 100644 index 0000000..187e053 --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x multiome (snRNA-seq and snATAC-seq).", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x multiome (snRNA-seq and snATAC-seq).\".
\nDescription: This dataset consists of raw sequencing snRNA-seq data and snATAC-seq data (10x Genomics Chromium Next GEM Multiome ATAC/GEX). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-and-permeabilisation-of-fresh-fro-n2bvj3yqnlk5/v1, https://cdn.10xgenomics.com/image/upload/v1728078404/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdf.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "30-09-2025", + "version": "1.0", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium\nLaboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium\nDepartment of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium\nKU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium\nVIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.\nDepartment of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.md b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.md new file mode 100644 index 0000000..867460e --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.md @@ -0,0 +1,64 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei RNA sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – 10x multiome (snRNA-seq and snATAC-seq).". + +## Dataset Description: + +This dataset consists of raw sequencing snRNA-seq data and snATAC-seq data (10x Genomics Chromium Next GEM Multiome ATAC/GEX). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-and-permeabilisation-of-fresh-fro-n2bvj3yqnlk5/v1, https://cdn.10xgenomics.com/image/upload/v1728078404/support-documents/CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevG.pdf.pdf. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium +Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium +KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium +VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium. +Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-multimodal, v1.0 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 30-09-2025 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.pdf b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.pdf new file mode 100644 index 0000000..682bcb4 Binary files /dev/null and b/WIP/voet-pmdbs-sn-multimodal/DOI/voet-pmdbs-sn-multimodal_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-multimodal/refs/Voet_pmdbs_sn_multimodal_Dataset_Information.docx b/WIP/voet-pmdbs-sn-multimodal/refs/Voet_pmdbs_sn_multimodal_Dataset_Information.docx new file mode 100644 index 0000000..ef619d0 Binary files /dev/null and b/WIP/voet-pmdbs-sn-multimodal/refs/Voet_pmdbs_sn_multimodal_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-multimodal/version b/WIP/voet-pmdbs-sn-multimodal/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-multimodal/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/10.5281_zenodo.18988761 b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/10.5281_zenodo.18988761 new file mode 100644 index 0000000..3ecc05d --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/10.5281_zenodo.18988761 @@ -0,0 +1,2 @@ +ALL_VERSIONS : https://doi.org/10.5281/zenodo.18988761 +CURRENT : https://doi.org/10.5281/zenodo.18988762 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/beta-deposition.json b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/beta-deposition.json new file mode 100644 index 0000000..0b7049e --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/beta-deposition.json @@ -0,0 +1,116 @@ +{ + "created": "2026-03-12T19:16:54.736838+00:00", + "modified": "2026-03-12T19:16:55.591007+00:00", + "id": 18988762, + "conceptrecid": "18988761", + "doi": "10.5281/zenodo.18988762", + "conceptdoi": "10.5281/zenodo.18988761", + "doi_url": "https://doi.org/10.5281/zenodo.18988762", + "metadata": { + "title": "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.", + "doi": "10.5281/zenodo.18988762", + "publication_date": "2026-03-12", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.\".
\nDescription: This dataset consists of raw sequencing snRNA-seq data using ParseBio Evercode Whole Transcriptome. The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://dx.doi.org/10.17504/protocols.io.8epv55xwdv1b/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a specific ParseBio barcode. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n\n\n", + "access_right": "open", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "version": "0.1", + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ], + "license": "cc-by-4.0", + "imprint_publisher": "Zenodo", + "upload_type": "dataset", + "prereserve_doi": { + "doi": "10.5281/zenodo.18988762", + "recid": 18988762 + } + }, + "title": "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and 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"project_description": "The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.", + "dataset_description": "This dataset consists of raw sequencing snRNA-seq data using ParseBio Evercode Whole Transcriptome. The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://dx.doi.org/10.17504/protocols.io.8epv55xwdv1b/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a specific ParseBio barcode. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "2026-03-12", + "version": "0.1", + "title": "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/version.doi b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/version.doi new file mode 100644 index 0000000..338797b --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988762 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio.json b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio.json new file mode 100644 index 0000000..dddf55e --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.\".
\nDescription: This dataset consists of raw sequencing snRNA-seq data using ParseBio Evercode Whole Transcriptome. The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://dx.doi.org/10.17504/protocols.io.8epv55xwdv1b/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a specific ParseBio barcode. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "2026-03-12", + "version": "0.1", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.md b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.md new file mode 100644 index 0000000..527deb7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.md @@ -0,0 +1,49 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei RNA sequencing (ParseBio) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients.". + +## Dataset Description: + +This dataset consists of raw sequencing snRNA-seq data using ParseBio Evercode Whole Transcriptome. The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://dx.doi.org/10.17504/protocols.io.8epv55xwdv1b/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a specific ParseBio barcode. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-rnaseq-parsebio, v0.1 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 2026-03-12 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.pdf b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.pdf new file mode 100644 index 0000000..2e13010 Binary files /dev/null and b/WIP/voet-pmdbs-sn-rnaseq-parsebio/DOI/voet-pmdbs-sn-rnaseq-parsebio_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/refs/Voet_pmdbs_sn_rnaseq_parsebio_Dataset_Information.docx b/WIP/voet-pmdbs-sn-rnaseq-parsebio/refs/Voet_pmdbs_sn_rnaseq_parsebio_Dataset_Information.docx new file mode 100644 index 0000000..3960049 Binary files /dev/null and b/WIP/voet-pmdbs-sn-rnaseq-parsebio/refs/Voet_pmdbs_sn_rnaseq_parsebio_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-rnaseq-parsebio/version b/WIP/voet-pmdbs-sn-rnaseq-parsebio/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq-parsebio/version @@ -0,0 +1 @@ +1.0 diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/10.5281_zenodo.18988768 b/WIP/voet-pmdbs-sn-rnaseq/DOI/10.5281_zenodo.18988768 new file mode 100644 index 0000000..e9455c5 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/DOI/10.5281_zenodo.18988768 @@ -0,0 +1,2 @@ +ALL_VERSIONS : https://doi.org/10.5281/zenodo.18988768 +CURRENT : https://doi.org/10.5281/zenodo.18988769 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/beta-deposition.json b/WIP/voet-pmdbs-sn-rnaseq/DOI/beta-deposition.json new file mode 100644 index 0000000..5e3de61 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/DOI/beta-deposition.json @@ -0,0 +1,116 @@ +{ + "created": "2026-03-12T19:17:06.033797+00:00", + "modified": "2026-03-12T19:17:06.422361+00:00", + "id": 18988769, + "conceptrecid": "18988768", + "doi": "10.5281/zenodo.18988769", + "conceptdoi": "10.5281/zenodo.18988768", + "doi_url": "https://doi.org/10.5281/zenodo.18988769", + "metadata": { + "title": "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.", + "doi": "10.5281/zenodo.18988769", + "publication_date": "2026-03-12", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.\".
\nDescription: This dataset consists of raw sequencing snRNA-seq data (10x Genomics Chromium Next GEM Single Cell 3\u02b9). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n\n\n", + "access_right": "open", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "version": "0.1", + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ], + "license": "cc-by-4.0", + "imprint_publisher": "Zenodo", + "upload_type": "dataset", + "prereserve_doi": { + "doi": "10.5281/zenodo.18988769", + "recid": 18988769 + } + }, + "title": "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.", + "links": { + "self": "https://zenodo.org/api/records/18988769", + "html": "https://zenodo.org/records/18988769", + "doi": "https://doi.org/10.5281/zenodo.18988769", + "parent_doi": "https://doi.org/10.5281/zenodo.18988768", + "badge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988769.svg", + "conceptbadge": "https://zenodo.org/badge/doi/10.5281%2Fzenodo.18988768.svg", + "files": "https://zenodo.org/api/records/18988769/files", + "bucket": "https://zenodo.org/api/files/3209175a-dce5-411b-aa32-75bfaa9d0fa0", + "thumb250": "https://zenodo.org/record/18988769/thumb250", + "thumbs": { + "10": "https://zenodo.org/record/18988769/thumb10", + "50": "https://zenodo.org/record/18988769/thumb50", + "100": "https://zenodo.org/record/18988769/thumb100", + "250": "https://zenodo.org/record/18988769/thumb250", + "750": "https://zenodo.org/record/18988769/thumb750", + "1200": "https://zenodo.org/record/18988769/thumb1200" + }, + 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acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis.", + "dataset_title": "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.", + "dataset_description": "This dataset consists of raw sequencing snRNA-seq data (10x Genomics Chromium Next GEM Single Cell 3\u02b9). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "publication_date": "2026-03-12", + "version": "0.1", + "title": "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.", + "ASAP_lab_name": "Aerts Lab", + "PI_full_name": "Stein Aerts", + "PI_email": "stein.aerts@kuleuven.be", + "submitter_name": "Gert Hulselmans", + "submitter_email": "gert.hulselmans@kuleuven.be", + "publication_DOI": "NA", + "grant_ids": [ + "ASAP-000430" + ], + "team_name": "Voet" +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/version.doi b/WIP/voet-pmdbs-sn-rnaseq/DOI/version.doi new file mode 100644 index 0000000..c1770f8 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/DOI/version.doi @@ -0,0 +1 @@ +10.5281/zenodo.18988769 \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq.json b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq.json new file mode 100644 index 0000000..4c07d9d --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq.json @@ -0,0 +1,64 @@ +{ + "metadata": { + "title": "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.", + "upload_type": "dataset", + "description": "This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
\n
This Zenodo deposit contains a publicly available description of the Dataset:
\nTitle: \"Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snRNA-seq.\".
\nDescription: This dataset consists of raw sequencing snRNA-seq data (10x Genomics Chromium Next GEM Single Cell 3\u02b9). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
\n\n", + "publication_date": "2026-03-12", + "version": "0.1", + "creators": [ + { + "name": "Pan\u010d\u00edkov\u00e1, Alexandra", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0693-132X" + }, + { + "name": "Theunis, Koen", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-0699-6676" + }, + { + "name": "Hulselmans, Gert", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-2205-1899" + }, + { + "name": "Sigalova, Olga", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0001-8598-1079" + }, + { + "name": "De Man, Julie", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0009-0003-7208-8961" + }, + { + "name": "Voet, Thierry", + "affiliation": "Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium", + "orcid": "0000-0003-1204-9963" + }, + { + "name": "Aerts, Stein", + "affiliation": "Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium", + "orcid": "0000-0002-8006-0315" + } + ], + "resource_type": "dataset", + "communities": [ + { + "identifier": "asaphub" + } + ], + "references": [ + "Aligning Science Across Parkinson's Collaborative Research Network Cloud, https://cloud.parkinsonsroadmap.org/collections, RRID:SCR_023923", + "Team Voet" + ], + "license": { + "id": "cc-by-4.0" + }, + "grants": [ + { + "id": "10.13039/100018231::ASAP-000430" + } + ] + } +} \ No newline at end of file diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.md b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.md new file mode 100644 index 0000000..8f22db0 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.md @@ -0,0 +1,49 @@ +This Zenodo deposit contains a publicly available description of the Dataset: + +# "Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – 10x snRNA-seq.". + +## Dataset Description: + +This dataset consists of raw sequencing snRNA-seq data (10x Genomics Chromium Next GEM Single Cell 3ʹ). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://dx.doi.org/10.17504/protocols.io.5qpvo1rddg4o/v1, https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors. + + +**Authors:** + +* Pančíková, Alexandra; [ORCID:0000-0002-0693-132X](0000-0002-0693-132X); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium,& Laboratory of Integrative Cancer Genomics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium,& Department of Oncology, KU Leuven, Leuven, Belgium +* Theunis, Koen; [ORCID:0000-0002-0699-6676](0000-0002-0699-6676); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Hulselmans, Gert; [ORCID:0000-0003-2205-1899](0000-0003-2205-1899); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Sigalova, Olga; [ORCID:0000-0001-8598-1079](0000-0001-8598-1079); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* De Man, Julie; [ORCID:0009-0003-7208-8961](0009-0003-7208-8961); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium +* Voet, Thierry; [ORCID:0000-0003-1204-9963](0000-0003-1204-9963); Department of Human Genetics, KU Leuven, Leuven, Belgium,& KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium +* Aerts, Stein; [ORCID:0000-0002-8006-0315](0000-0002-8006-0315); Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium,& VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,& Department of Human Genetics, KU Leuven, Leuven, Belgium + + +**ASAP Team:** Voet + +**Dataset Name:** voet-pmdbs-sn-rnaseq, v0.1 + +**Principal Investigator:** Stein Aerts, stein.aerts@kuleuven.be + +**Dataset Submitter:** Gert Hulselmans, gert.hulselmans@kuleuven.be + +**Publication DOI:** NA + +**Grant IDs:** ['ASAP-000430'] + +**ASAP Lab:** Aerts Lab + +**ASAP Project:** Understanding inherited and acquired genetic variation in Parkinson's disease through single-cell multi-omics analyses: a unique data resource + +**Project Description:** The functional roles of inherited and acquired genetic variation in the pathogenesis of Parkinson's disease (PD) remain largely unknown. Here, we will first study how germline genetic variants at PD-risk loci, which were identified by genome-wide association study (GWAS), perturb the expression of genes in specific cell (sub)populations of the brain and gut. To this aim, we will apply single-cell gene-expression and open-chromatin quantitative trait locus (QTL) analyses, enabling identification of PD-relevant genes and cell (sub)types. We will deliver the mechanisms of PD-candidate gene expression (dys)regulation in the normal condition, with ageing and in PD, as well as a unique single-cell multi-omic resource for the community. Second, we will study the nature and role of somatic mutations in brain and gut cells in PD- etiopathology. Finally, we will characterize biochemical and phenotypic effects of loss- or gain-of-function QTLs and somatic mutations of candidate genes in in vitro and in vivo model systems, including their impact on the neuro-immune axis. + +**Submission Date:** 2026-03-12 + +__________________________________________ + + +> This dataset is made available to researchers via the ASAP CRN Cloud: [cloud.parkinsonsroadmap.org](https://cloud.parkinsonsroadmap.org). Instructions for how to request access can be found in the [User Manual](https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf). + +> This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). + +> This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset + diff --git a/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.pdf b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.pdf new file mode 100644 index 0000000..be10a9c Binary files /dev/null and b/WIP/voet-pmdbs-sn-rnaseq/DOI/voet-pmdbs-sn-rnaseq_README.pdf differ diff --git a/WIP/voet-pmdbs-sn-rnaseq/refs/Voet_pmdbs_sn_rnaseq_Dataset_Information.docx b/WIP/voet-pmdbs-sn-rnaseq/refs/Voet_pmdbs_sn_rnaseq_Dataset_Information.docx new file mode 100644 index 0000000..d5867fd Binary files /dev/null and b/WIP/voet-pmdbs-sn-rnaseq/refs/Voet_pmdbs_sn_rnaseq_Dataset_Information.docx differ diff --git a/WIP/voet-pmdbs-sn-rnaseq/version b/WIP/voet-pmdbs-sn-rnaseq/version new file mode 100644 index 0000000..d3827e7 --- /dev/null +++ b/WIP/voet-pmdbs-sn-rnaseq/version @@ -0,0 +1 @@ +1.0This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual.
\nThis research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF).
\nThis Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset
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