RNA-seq Analysis of Sorted and Bulk Cell Cultures

For gene expression analysis, total RNA was collected using the mirVana RNA isolation kit (ThermoFisher Scientific) or RNeasy Mini Kit (Qiagen) from sorted (>20,000 cells) and bulk cultures (>1,000,000 cells). Illumina libraries were constructed using the TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina). Finally, libraries were quantified using Fragment Analyzer (Advanced Analytical). RNA-seq libraries were sequenced with HiSeq 4000 (Illumina) using a 2x76bp read length and alignment was performed using STAR Aligner^{92 (link)} against the GRCh38 reference genome. Gene counts were obtained using featureCounts^{93 (link)} and FPKM per gene were calculated using Cufflinks^{94 (link)}. Values were normalized using quantile normalization.