Raw gene counts, gene expression values and single cell matrix files used in the study.

Quality control analysis of fastq raw data was performed using FastQC [93]. Reads were aligned to reference genome (hg38) using STAR, and reads were quantified using HTSeq-counts with Gencode annotation v38 and raw counts provided in Table 2a. Differential expression analysis was performed with DESeq. For differential gene expression analyses, the cutoff for significant fold change was >1.5, adjusted p-value <0.05 and provided in Table 2b. Single cell data: After samples were demultiplexed, individual fastq files were subjected to barcode processing and UMI counting using Cell Ranger v2.1.0 (https://support.10xgenomics.com). Each individual library was processed using cellranger count function to generate a gene-barcode matrix for each library and reads aligned to the human reference genome (hg38). Cell barcodes and UMIs associated with the aligned reads were subjected to correction and filtering using an estimation of 3000 recovered cells (—expect-cells 3000). The resulting gene-cell UMI count matrices for each sample were then concatenated into one matrix using the “cellranger aggr” pipeline and files are provided as compressed files in Table 2c.
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