Transcriptional landscape of pathogen-responsive lncRNAs in primary mammary epithelial cells reveals insights in immune response and defense mechanism.

RNA-seq was performed by infecting primary mammary epithelial cells (pMECs) with both gram negative (E.coli) and gram positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control. lncRNA profiles of primary mammary epithelial cells (pMECs) were generated by deep sequencing, in triplicate, using Illumina 2500 platform. The sequence reads that passed quality filters were analyzed at the transcript level withTopHat followed by Cufflinks. lncRNAs were identified using four independent algorithms i.e., CNCI, PLEK, CPAT and PFAM. qRT–PCR validation was performed using SYBR Green assays.