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. heart mRNA profiles of 3 different stages of MI (1D, 1W, 8W) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.本研究通过对8周龄雄性C57BL/6小鼠实施左前降支冠状动脉（left anterior descending coronary artery, LAD）永久结扎术，构建心肌梗死（Myocardial infarction, MI）模型。分别于心肌梗死后1天（1D）、1周（1W）及8周（8W）采集小鼠左心室（left ventricle, LV）组织，用于构建cDNA文库。对于RNA测序（RNA-sequencing），使用Illumina公司的TruSeq RNA文库构建试剂盒，以从心肌梗死模型组与假手术（sham）组小鼠的混合左心室组织中提取的1μg总RNA为模板构建cDNA文库。针对小RNA测序（small RNA-sequencing），先采用Qiagen公司的miRNeasy Mini试剂盒从上述两组小鼠的混合左心室组织中提取1μg总RNA，随后使用Illumina公司的TruSeq RNA文库制备试剂盒完成小RNA文库构建。总RNA与小RNA的表达谱均通过Illumina HiSeq 2000测序仪完成三次生物学重复的深度测序获得。RNA测序的读段通过整合Bowtie v2.2.3算法的Tophat v2.0.13工具，比对至小鼠（Mus musculus）参考基因组mm10版本。将读段比对至基因组后，使用Cufflinks v2.2.1工具将比对后的读段组装为转录本并估算其表达丰度。小RNA测序的读段通过miRDeep2算法，比对至miRBase v21数据库中获取的小鼠成熟miRNA及前体miRNA序列。采用SYBR Green荧光定量PCR（qRT–PCR）完成表达验证实验。RNA测序的总比对读段均值为33,951,175，整体读段比对率为96.84%。在RNA测序的转录本表达定量环节，将基因的读段计数归一化为FPKM值。所有mRNA的归一化读段计数的散点图（R²>0.99）显示生物学重复之间具有极高的相关性，表明实验具备良好的可重复性。本数据集涵盖心肌梗死三个不同阶段（1D、1W、8W）的小鼠心脏mRNA表达谱，均通过Illumina HiSeq 2000测序仪完成三次生物学重复的深度测序获得。

搜集汇总

背景与挑战

背景概述

该数据集包含心肌梗死小鼠模型的心脏RNA测序数据，通过高通量测序分析mRNA和小RNA在MI后1天、1周和8周的表达变化。实验使用C57BL/6雄性小鼠，采用Illumina HiSeq 2000平台进行深度测序，每个时间点设有三个生物学重复，数据质量控制良好（总比对读数约3400万，比对率96.84%，重复性高R2 > 0.99），旨在研究MI不同阶段的转录组动态。