RNA-sequencing data of mouse heart in myocardial infarction

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. Overall design: heart mRNA profiles of 3 different stages of MI (1D, 1W, 8W) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.