RNA Sequencing dataset of Claudin-low Breast Cancer Cell Lines with Neuropilin-1 Knockdown

Triple-negative breast cancers (TNBC) are a particularly aggressive breast cancer subtype with poor prognosis and high relapse rates. Due to a lack of identified targeted therapies, chemotherapy currently remains as the primary treatment for TNBC. Approximately 25-39% of TNBC are claudin-low breast cancers, which are mainly defined by low expression of cell-cell adhesion proteins and enrichment of mesenchymal signatures. Functional studies have demonstrated the potential role of the transmembrane-coreceptor, Neuropilin-1 (NRP1) in regulating the progression of these tumours. However, there have been no high-throughput studies to date that comprehensively investigate NRP1-modulated cell signalling across multiple claudin-low cell lines. Therefore, we knocked-down NRP1 by two small-interfering RNA (siRNA) or two short-hairpin RNA (shRNA) sequences in each of HS578T, MDA-MB-231 and SUM159PT claudin-low cell lines and followed this with Bulk-RNA sequencing. We present this comprehensive transcriptomic data set which provides a valuable resource for the analysis of NRP1-regulated signalling pathways in claudin-low breast cancer, paving the way for future studies of its potential as a targeted therapeutic. Overall design: 52 samples. 2-3 biological replicates of each treatment group. Three claudin-low breast cancer cell lines (HS578T, MDA-MB-231, SUM159PT) were treated with two siRNA and two shRNA sequences (3 and 5) that target NRP1, as well as respective non-targeting (NT) controls.