RNA-seq analysis of human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7) or MYC

We profiled gene expression and splicing changes in HCC1806 human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7), all three splicing factors (called 3xSR) or MYC. We performed RNA-seq, in triplicate on 3xSR, MYC-OE, triple plasmid control, SRFS2, SRSF3, SRSF7, or single plasmid control HCC1806 cells. Overall design: 2D-grown HCC1806 cells were harvested by scraping adherent cells in PBS once ~90% confluence was reached. Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions. Barcoded RNA libraries were prepared starting with 500ng of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent). Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina NovaSeq, equal amounts of 18 libraries were pooled per lane.