RatTransc: a rat long noncoding RNA database ===================== INTRODUCTION ===================== Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads in combination with RefSeq and UniGene annotated RNAs, we identify 39,154 lincRNA transcripts encoded by 19,162 lincRNA genes in the rat. We reveal sequence and expression similarities in lincRNAs of rat, mouse and human. The DNA methylation level of lincRNAs is higher than that of protein-coding genes across the transcription start sites (TSSs). And, three lincRNA genes overlap with differential methylation regions (DMRs) which associate with spontaneously hypertensive disease. In addition, there are similar binding trends for three transcription factors (HNF4A, CEBPA and FOXA1) between lincRNA genes and protein-coding genes, indicating that they harbour similar transcription regulatory mechanisms. To date, this is the most comprehensive assessment of lincRNAs in the rat genome. We provide valuable data that will advance lincRNA research using rat as a model. ===================== Download ===================== Rat (Rattus norvegicus) lincRNAs -- Rat lincRNAs (on Rnor_6.0 in GFF3 format) -- Rat lincRNAs (on Rnor_6.0 in GTF format) -- Rat lincRNAs (on Rnor_6.0 in BED format) -- Rat lincRNAs (in fasta format) Rat (Rattus norvegicus) gene expression -- Rat FPKM expression levels, derived from SRP037986 using TopHat and Cufflinks -- Rat FPKM gene expression levels, derived from SRP041119 using TopHat and Cufflinks -- Rat count gene expression levels, derived from SRP037986 using SummaryOverlaps -- Rat count expression levels, derived from SRP041119 using SummaryOverlaps Rat (Rattus norvegicus) tissue-specific gene expression -- rat_gene_differential_expression_SRP041119.txt.tar.gz -- rat_gene_differential_expression_SRP037986.txt.tar.gz Blasting Rat (Rattus norvegicus) lincRNAs agains human and mouse lncRNAs -- rat_lincRNAs_blast_mouse_gencodevM9_lncRNAs.txt.tar.gz -- rat_lincRNAs_blast_human_gencodev24_lncRNAs.txt.tar.gz Other publications that identified rat lncRNAs [1] Leung, A. et al. Novel Long Noncoding RNAs Are Regulated by Angiotensin II in Vascular Smooth Muscle CellsNovelty and Significance. Circulation research 113, 266-278 (2013). -- original dataset PMID23697773_RN4_lncRNAs.bed | Rnor_6.0 dataset PMID23697773_RN6_lncRNAs.bed [2] Wang, F. et al. Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat. Scientific reports 4, 7146 (2014). -- original dataset PMID25413633_RN5_lncRNAs.bed | Rnor_6.0 dataset PMID25413633_RN6_lncRNAs.bed [3] Gopalakrishnan, K., Kumarasamy, S., Mell, B. & Joe, B. Genome-Wide Identification of Long Noncoding RNAs in Rat Models of Cardiovascular and Renal DiseaseNovelty and Significance. Hypertension 65, 200-210 (2015). -- original dataset PMID25385761_RN5_lncRNAs.bed | Rnor_6.0 dataset PMID25385761_RN6_lncRNAs.bed ===================== COPYING ===================== GNU Public License version 3 (GPLv3) Details on http://www.gnu.org/copyleft/gpl.html
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