RNA-Seq of Homo sapiens;Triple negative breast cancer: Sample TNBC3
Total RNA was isolated from tumors, normal breast tissues, and PDXs using the RNeasy Plus Mini kit (Qiagen), with additional on-column DNase treatment to eliminate traces of genomic DNA. mRNAseq libraries were made from total RNA using the Illumina TruSeq mRNA sample preparation kit and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration. Purity-filtered reads were aligned to the human reference GRCh38/hg38 genome using Spliced Transcripts Aligned to a Reference (STAR) version 2.4.2a1. Transcript (GENCODE v22) abundance estimates were generated by Salmon version 0.6.02 in '-quant' mode, based on the STAR alignments. Raw read counts for all RNAseq samples were normalized to a fixed upper quartile3. RNAseq normalized gene counts were then log2 transformed (zeros were unchanged), and genes were filtered for those expressed in 70% of samples.