RNA-Sequencing of LBH transcriptomes in human breast cancer cell lines

Purpose: Gene expression analysis of knockdown and overexpression of LBH (Limb-Bud-and-Heart) in human breast cancer cell lines using RNA-Seq Methods: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector) for LBH overexpression (OE) in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected and analyzed from three biological replicates of each condition (siLBH vs non-target/NT siRNA) for LBH knockdown (KD) in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). High-throughput sequencing used Illumina platforms. Results: Using an optimized data analysis workflow, we mapped about 60 million sequence reads per sample to the human genome (build hg19). Conclusions: Our study represents the first gene profiling analysis of LBH transcriptomes in human breast cancer cell lines, with biologic replicates, generated by RNA-seq technology. Overall design: RNA was collected and analyzed from three biological replicates of each condition (LBH vs vector control) for LBH overexpression in two human breast cancer cell lines (BT549, MCF7). Additionally, RNA was collected and analyzed from three biological replicates of each condition (siLBH vs scramble siRNA control) for LBH knockdown in two human triple negative breast cancer cells lines (HCC1395, MDA-MB-231). The resulting sequenced reads were mapped. Comparisons of transcriptomes between the different study groups allow identification of LBH regulated genes which may underly breast cancer progression.