Sequencing analysis of proliferative heterogeneity in squamous cell carcinomas

ChIP-seq, ATAC-seq and RNA-seq analyses were integrated to define direct, transcriptional Tgfβ targets in quiescent tumor propogating cells 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 TGFβ1. Copy number variation (CNV) analyses were done on input samples and nonsynonymous mutations were called from RNAseq data.