Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 24h in the presence of androgen

The aim of this study was to use NGS RNAseq deep-sequencing in order to characterize the polyadenylated mRNAs and lncRNAs expressed in LNCaP cells treated with androgen hormone compared with untreated LNCaP cells (GSE79301). Trimmed reads were mapped using the hg19 genome with TopHat v.2.0.12 and Bowtie v.2.2.3. The assembly was guided by a custom GTF file created with transcripts fromhuman lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013). The diferencial expression was calculated by the sum of exon read count per gene with HTSeq (Anders, Pyl et al. 2015), followed by a DESeq2 analysis (Love, Huber et al. 2014). Overall design: polyA+ RNA profiles of LNCaP prostate cancer cell line grown in culture for 24h in the presence of 1 nM of the synthetic androgen R1881 and than were generated by paired-end deep sequencing, in duplicate, using Illumina HiSeq2000. This series contains re-analyzed samples from GSE79301.