ISAC1

Title: Systems-level Immunomonitoring in Children with Solid Tumors

Description

This repository contains scripts and data needed to reproduce the figures in the paper Systems-level Immunomonitoring in Children with Solid Tumors.

Repository Structure

• Data/: Contains all processed tables required for reproducing the figures in the paper.
• Scripts/: Contains code to regenerate the figures presented in the paper.

Data Availability

Single-Cell RNA Sequencing

Data are available at Mendeley Data in .h5Seurat format. To regenerate the processed tables in the Data/ folder, place the data under single cell data/ and run the preparation.R script located in the folder.

Single-Cell TCR Sequencing

The processed single-cell TCR sequencing table is available as Data/scTCR_data_merge_paired_chain_from_tan_20240415.csv.gz. scTCR and scRNA tables can be linked via the column unique_index. The raw sequencing files are sensitive and available upon reasonable request.

Adult Data from Public Datasets

Original data from adult datasets are from Wu et al. Nature 2020, Zhang et al. Nature 2018 and Guo et al. Nature Medicine 2018. The processed data for peripheral memory CD8+ T cells used in this paper can be accessed at Mendeley Data. To regenerate the processed tables in the Data/ folder, place the data under single cell data/ and run the preparation.R scripts.

CyTOF

Raw FCS files are available at FlowRepository (ID: FR-FCM-Z8C8).

Plasma Protein (Olink)

Processed Normalized Protein eXpression (NPX) data is available as Data/olink_npx_baseline.csv.

Metadata of Patients

Patient metadata can be found in the file Data/metadata.csv.

Tissue Sequencing

Bulk RNAseq count data can be found at Data/count_to_tpm_remove_batch_deseq2_normalized_new_meta20240903.csv.
MAF format of somatic variants from whole genome sequence can be found at Data/isac1_filtered_all_135_samples_maf_maftools.maf.
TCR sequences estimated by TRUST4 for blood bulk RNAseq and tumor tissue bulk RNAseq locate at Data/blood_tissue_tcr_from_trust_merge.tsv and Data/tumor_tissue_tcr_from_trust_merge.tsvrespectively.

Dependencies

To reproduce the figures, the following R version and packages are required:

• R version: 4.2.3
• Packages: dplyr 1.1.2, readr 2.1.4, ggplot2 3.4.4, ggpubr 0.6.0, ggalluvial 0.12.5, ggrepel 0.9.3, wesanderson 0.3.6, ComplexHeatmap 2.14.0, pheatmap 1.0.12, EnhancedVolcano 1.16.0, Seurat 4.3.0, SeuratDisk 0.0.0.9020, rstatix 0.7.2, parallel 4.2.3, igraph 1.4.1, pROC 1.18.5, corrplot 0.92, caret 6.0-94, lattice 0.22-5, relaimpo 2.2-7, paletteer 1.6.0, robCompositions 2.4.1, data.table 1.14.8, pls 2.8-3, ggridges 0.5.6, webr 0.1.5, lubridate 1.9.3, forcats 1.0.0, stringr 1.5.1, purrr 1.0.2, tidyr 1.3.0, tibble 3.2.1, tidyverse 2.0.0, mitools 2.4, survey 4.2-1, survival 3.5-7, Matrix 1.5-1, boot 1.3-28.1, MASS 7.3-60.

To install the required packages, run the following command in R:

install.packages(c("dplyr", "readr", "ggplot2", "ggpubr", "ggalluvial", "ggrepel", 
                   "wesanderson", "ComplexHeatmap", "pheatmap", "EnhancedVolcano", 
                   "Seurat", "SeuratDisk", "rstatix", "parallel", "igraph", "pROC",
                   "corrplot", "caret", "lattice", "relimpo", "paletteer", "robCompositions",
                   "data.table", "pls", "ggridges", "webr", "lubridate", "forcats", 
                   "stringr", "purrr", "tidyr", "tibble", "tidyverse", "mitools", 
                   "survey", "survival", "Matrix", "boot", "MASS"))

Contact

For any issues or questions regarding data analyses, please contact petter.brodin@ki.se.