Whole transcriptome sequencing
Description
Whole transcriptome sequencing data and ceRNA regulatory network profiling of heat acclimation in protecting against heat stress-induced myocardial injury in rat myocardium
Files
Steps to reproduce
Total RNA from the myocardium of rats was extracted using TRIzol reagent (Invitrogen, NY, USA). Prior to sequencing, RNA samples were assessed for both quantitative and qualitative integrity using Qubit (Thermo company) and by performing 1% agarose electrophoresis. The purified RNA was subsequently stored at –80°C. RNA samples were then submitted to Jenergy Biotechnology Shanghai Co., Ltd (China) for RNA sequencing. Two-ended sequencing mode was performed on the Illumina nova6000 platform, following the manufacturer’s instructions, and using the nova6000S4 sequencing reagent PE150 (Illumina, USA). The study employed high-throughput sequencing of numerous samples, utilizing an insert size of 300–450 bp to generate the ultimate cDNA library. Additionally, the miRNA library was prepared using Illumina’s TruSeq® miRNA Sample Prep Kit v2 and subjected to single terminal 50 bp sequencing mode on the Illumina HiSeq 6000 high-throughput sequencing platform.The fragments per kilobase of transcript per million reads mapped value was used to determine mRNA and lncRNA expression levels, the back spliced reads per billion mapping reads value was utilized to quantify circRNAs, and the counts per million metrics was used to measure miRNA abundance. Differential expression analysis was conducted using DESeq2(v1.16.1), with screening conditions uniformly set to |log2(fold change)| ≥ 1 and P < 0.05 to determine significant differential expression. GO biological function enrichment and KEGG signaling pathway enrichment were performed to elucidate the role of differentially expressed mRNAs and the potential target genes of lncRNAs, circRNAs, and miRNAs in the context of HA against HS. The p-value of GO and KEGG enrichment was adjusted using Fisher’s Exact Test method.
Institutions
- Academy of Military Medical Sciences