Sequencing analysis of proliferative heterogeneity in squamous cell carcinomas

ChIP-seq, ATAC-seq and RNA-seq analyses were integrated to define direct, transcriptional Tgfß targets in quiescent tumor propogating cells Overall design: Differential gene expression analyses were performed between quiescent (CD71lo H2BGFPhi), proliferative (CD71hi H2BGFPlo) and double negative (CD71lo H2BGFPlo) cells in two independent tumors. ATAC-seq analysis were compared between proliferative states depending on CD71 expression and H2BGFP label retention. Smad2/3 ChIP-seq analysis was performed on cells growth arrested in vitro with 5ng/mL TGFß1. Copy number variation (CNV) analyses were done on input samples and nonsynonymous mutations were called from RNAseq data.