This repo is associated with our SCPA paper published in Cell Reports
The repo contains all the R scripts to replicate figures of the paper, and bulk RNA-seq analysis of Ifnar1-/- mice.
Raw and processed sequencing data for both bulk and scRNA-seq can be found at GSE212270 and SRA PRJNA874734.
GSE212270 data contain:
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scRNA-seq data:
- GSE212270_RAW.tar containing matrix, features, and barcode files for each sample
- Seurat object .rds file for each sorted T cell population, integrated across the three time points (i.e. Naive CD4+ T cells at 0, 12, and 24 hours integrated, then Memory CD4+ T cells at 0, 12, and 24 hours integrated...)
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Bulk RNA-seq data
- GSE212270_counts.txt.gz containing featureCounts output of Ifnar1-/- versus WT bulk RNA-sequencing
- GSE212270_tmm_cpm_normalised.csv.gz containing TMM-adjusted CPM normalised values of edgeR processed Ifnar1-/- versus WT bulk RNA-sequencing