RNA-Seq analysis identifies pancreatic lncRNAs

Aim: Identification of long noncoding RNAs using transcriptional analysis of e15.5 mouse embryonic pancreas and adult mouse islets Methods: rRNA-depleted total RNA from e15.5 embryonic mouse pancreata and 12-week-old mouse islets was prepared using the Ribo-Zero rRNA removal kit. Biological replicates indicate that each RNA-seq data set was generated from individual mice (islets) or 3-4 pooled e15.5 embryonic pancreata. Libraries were prepared with Illumina TruSeq RNA sample preparation kit and then sequenced with 60 million, 2 x 100 paired reads on an Illumina HiSeq 2000 V3 instrument. To reconstruct the transcriptomes, we first mapped all reads of total RNAs to the mouse reference genome (mm10) with TopHat v1.3.2 (Trapnell et al., 2012). Cufflinks (v1.2.1) was subsequently applied to assemble the whole transcriptome and to identify all possible transcripts. Significantly differentially expressed genes were calculated using DEseq2. LncRNA and mRNA profiles of the e15.5 mouse pancreas and 12-week-old adult mouse islets were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.