fix wip voet datasets from metadata repo

WIP/voet-pmdbs-sn-atacseq-10x/DOI/10.5281_zenodo.18988729

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+ALL_VERSIONS        : https://doi.org/10.5281/zenodo.18988729
+CURRENT             : https://doi.org/10.5281/zenodo.18988730

WIP/voet-pmdbs-sn-atacseq-10x/DOI/beta-deposition.json

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+{
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+  "modified": "2026-03-12T19:16:15.865673+00:00",
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+    "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.",
+    "doi": "10.5281/zenodo.18988730",
+    "publication_date": "2026-03-12",
+    "description": "<p>This Zenodo deposit contains a publicly available description of the Dataset:</p>\n<p><strong>Title:</strong> \"Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients \u2013 10x snATAC-seq.\".</p>\n<p><strong>Description:</strong> 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.</p>\n\n\n<blockquote>\n<p>This dataset is made available to researchers via the ASAP CRN Cloud: <a href=\"https://cloud.parkinsonsroadmap.org\">cloud.parkinsonsroadmap.org</a>. Instructions for how to request access can be found in the <a href=\"https://storage.googleapis.com/asap-public-assets/wayfinding/ASAP-CRN-Cloud-User-Manual.pdf\">User Manual</a>.</p>\n<p>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).</p>\n<p>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</p>\n</blockquote>",
+    "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": [
+      {
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WIP/voet-pmdbs-sn-atacseq-10x/DOI/dataset.doi

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+10.5281/zenodo.18988729

WIP/voet-pmdbs-sn-atacseq-10x/DOI/project.json

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+{
+    "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"
+}

WIP/voet-pmdbs-sn-atacseq-10x/DOI/version.doi

@@ -0,0 +1 @@
+10.5281/zenodo.18988730