GSE196123
RAN-seq analysis comparing gene expression difference between control and Decr2 knock-down B16.SIY tumors
Purpose: To undstand the mechanism by which Decr2 knock-down tumors were resistant to CD8+ T cell killing in vitro and anti-PD-L1 therapy in vivo, we performed RNA-seq analysis comparing Decr2-knockdown versus control B16.SIY cells Methods: mRNA was isolated from Decr2 shRNAs (2 shRNA) and Control shRNA infected B16.SIY cells. mRNA profiles were generated by deep sequencing, in triplicate, using the Illumina HiSeq  platform. Alignment was performed using the Kallisto software.  All submitted samples passed quality control using the R package FastQC. Raw read counts were processed by TMM normalization followed by log2 transformation. Limma voom was used to identify differentially expressed genes between DECR2 knockdown and control cells. Overall design: RNA-seq was performed to compare the mRNA expression level between  Decr2 shRNAs and Control shRNA infected B16.SIY cells.