RNA-sequencing of human mammary epithelial cells (HMLEs) transduced in vitro with a shRNA against SOX4 or a scrambled shRNA in untreated and TGF-β-treated (16 hours) conditions

In order to identify SOX4- and TGF-beta dependent genes, human mammary epithelial cells (HMLEs) were transduced with shRNA scrambled (control) or shRNA targeting SOX4 (TRCN0000018213, Sigma Aldrich, St. Louis, MS) and selected with puromycin for at least 2 weeks. SOX4 knockdown was confirmed by qRTPCR and western blotting. Cells were plated in 6 well plates and either left untreated or treated with TGF-beta (2.5ng/ml) for 16 hours in biological duplicate (different passages). Samples were harvested and total RNA was isolated using RNAeasy kit (Qiagen). Samples were sequenced on the NextSeq 500 (Illumina), SE75. Through RNA-sequencing we analysed the differentially expressed genes upon in vitro knockdown of SOX4 and TGF-β pathway activation in human mammary epithelial cells using one shRNA against SOX4