RNA-seq profiling of transcriptomes of control and Hif1a mutant E12.5 hearts

Purpose: to identify genes aberrantly expressed upon myocardial ablation of Hif1a Methods: a floxed Hif1a allele was deleted in mouse embryonic hearts using a NXK2.5Cre line. Total RNA was extracted from E12.5 hearts (n=3 for controls and mutants) using Trizol and processed for RNA-seq. Reads were mapped to Mm10 reference genome using TopHat2 and Bowtie2. Transcript expression values were determined after transcript normalization with AltAnalyze Results: this analysis revealed a total of 1451 genes significantly (|> 20% and P<0.05) modulated in Hif1a cKO hearts 6 total RNAseq runs with 3 experimental samples and 3 controls samples研究目的：鉴定心肌组织中缺氧诱导因子1α（Hif1a）基因消融后异常表达的基因。 研究方法：采用NXK2.5Cre品系小鼠，在小鼠胚胎心脏中敲除携带floxed位点的Hif1a等位基因。使用Trizol试剂从E12.5胎鼠心脏提取总RNA（对照组与突变组各3例样本），并开展RNA测序（RNA-seq）。采用TopHat2与Bowtie2软件将测序reads比对至Mm10参考基因组。通过AltAnalyze完成转录本标准化分析后，计算转录本表达量。 研究结果：本次分析共鉴定出1451个在Hif1a条件性敲除（conditional knockout，cKO）胎鼠心脏中发生显著表达变化的基因（表达差异幅度>20%且P<0.05）；本实验共完成6次RNA测序，其中实验组与对照组样本各3例。