Total RNA seq in the human control and faling hearts

Purpose: In the present study, we aimed to identify novel lncRNAs associated with HF. Methods: We used left ventricular biopsies obtained from 21 explanted failing hearts and 5 non-failing control hearts. Deep RNA sequencing was performed on cardiac biopsies. RNA-seq data were aligned to human reference genome hg19 using TopHat. Differential expression analyses were conducted using the cufflinks and the DESeq2 algorithm. Results: An average of 211 million reads of total-RNA-seq librairies were generated. From these data, we identified a panel of 3247 lncRNAs that were either cardiac-enriched or differentially expressed between failing and non-failing hearts identified by either Cufflinks or DESeq2, including 1036 novel lncRNAs (i.e. not described in the GENCODE version 19 database). 232 of them were derived from novel genes and were from moderately to highly expressed in at least half samples. The novel gene derived lncRNAs differentially expressed in failing heart could correlate to at least one heart failure associated genes with a Spearman's rank correlation coefficient more than 0.7 or less than -0.7 in either ICM or DCM group.