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RNA-sequencing data of mouse heart in myocardial infarction

ABSTRACT: Myocardial infarction (MI) was induced by permanent ligation of the left anterior descending coronary artery (LAD) in 8 weeks C57BL/6 male mice. 1 day (1D), 1 week (1W), 8 weeks (8W) after MI, the mouse left ventricles were used to construct cDNA libraries. For RNA-sequencing, 1 μg of total RNA extracted from pooled mouse LV (left ventricle) of MI or sham animals was used to construct cDNA libraries using the TruSeq RNA library kit (Illumina). For small RNA-sequencing, 1 μg of total RNA from the pooled LV of MI and sham was isolated using a miRNeasy Mini kit (Qiagen) and libraries were prepared using a TruSeq RNA library preparation kit (Illumina). Total RNA and small RNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 sequencer. The reads from the RNA-seq were aligned to Mus musculus (mm10) using Tophat v2.0.13 which incorporates the Bowtie v2.2.3 algorithm. After aligning the reads to the genome, Cufflinks v2.2.1 was used to assemble aligned reads into transcripts and to estimate their abundance. The reads from small RNA-seq were aligned to Mus musculus matured and precursor miRNAs obtained from miRBase v21 using the miRDeep2 algorithm. qRT–PCR validation was performed using SYBR Green assays. The mean numbers of the total mapped reads by RNA-seq were 33,951,175 and the overall read mapping ratios were 96.84%. For the transcript expression quantification in RNA-seq, the number of reads for the genes were normalized to FPKM. Scatter plots of the normalized read counts of all mRNA (R2 > 0.99) showed high degrees of correlation between biological replicates, indicating their high levels of reproducibility.

ORGANISM(S): Mus musculus

PROVIDER: GSE114695 | GEO | 2020/04/14

REPOSITORIES: GEO

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Project description:We studied the long-term effects of single whole-body gamma and simulated GCR irradiation (IR) and consumption of a Western Diet (WD) on the heart's left ventricle (LV). Three-month-old C57Bl/6J wild-type male and female mice were assigned to the following groups: 1) Gamma-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 2) simGCRsim-irradiated with follow-up at 440(males and females) and 660(males)/550(females) days post-IR; 3) 270-days WD-fed animals with followup at 530 (males and females) and 750(males)/640(females). Control groups consisted of non-irradiated (non-IR) mice and normal diet-fed mice. Control groups were followed up similarly to the treatment groups. LV tissues were collected at follow-up and subjected to bulk RNA sequencing analysis. Total RNA was extracted from LV tissues using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and stored at -80°C until further use. A poly-A selected mRNA library was prepared using the NEBNextUltra™II RNA Library Prep Kit. The sequencing was performed on the Illumina NovaSeq-6000 platform to collect an average of 48 million 2x150bp paired-end reads per sample.FastQC (version 0.11.9) was used for the quality assessment of raw sequencing reads (Q30% was greater than 94%). Next, we aligned the reads to the mouse reference genome (mm39) with STAR aligner (version 2.7.8a) with gene count quantification mode and obtained raw gene counts. Differential gene expression analysis and functional annotation were performed using DeSeq2 and fgsea R packages. The results of the studies provide insight into the long-term transcriptome disturbance in response to irradiation and the Western diet, their association with structural and functional changes in LV, and implications in the development of cardiovascular disease (CVD). Furthermore, the study results pointed to the strong sex-biased pathophysiological and transcriptomic changes in LV.

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RNA-sequencing data of mouse heart in myocardial infarction

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