PRJNA674499
Identification of differential expression lncRNAs between chicken myoblasts and myotubes
The goal of this study is to identificate the differential expression lncRNAs between chicken myoblasts and myotubes using high-throughput sequencing technology.LncRNAs expression profiles of chicken myoblasts (GM) and myotubes (DM) were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. Index of the reference genome was built using bowtie 2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.4. HISAT2 was run with '-rna-strandness RF', other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) in a reference-based approach. Transcripts coding potential were analyzed by CPC, Pfam-sca, and phyloCSF. Transcripts predicted with coding potential by all of the three tools above were filtered out, and those without coding potential were our candidate set of lncRNAs.Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the chicken reference genome (GRCg6a) and identified 6878 lncRNAs in chicken myoblasts (GM) and myotubes (DM). 29 lncRNAs showed differential expression between GM and DM, with q value <0.05. 10 lncRNAs showed up-regulated and 19 lncRNAs showed down-regulated in DM VS GM.