Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers, Chunhong Zheng et. al
Description
RNA-Seq data from 10 patients in "Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers" (Cancer Cell manuscript). "patientRNAexp.tsv" is FPKM values from Cufflinks, for 10 bulk tumor RNA-Seq samples. "CRI3571.10X.counts.csv.gz" is 10X single cell gene expression data from Cell Ranger's 'count' command. "CRI????_CD?.SS2.counts.csv.gz" are Smart-seq2 gene expression data from TraCeR (summarized from transcript to gene level).
Files
Steps to reproduce
For bulk RNA-Seq, used STAR to align adapter-trimmed reads to hg19, then Cufflinks to generate FPKM values per transcript, then assigned median transcript FPKM to each gene (symbol). For 10X scRNA-Seq, used Cell Ranger 'count' command. For SS2 scRNA-Seq, used TraCeR to generate per-transcript counts, then custom R code to summarize to gene level counts.