GSE54132
Genome-wide profiling of gene expression under electro-acupuncture treatment on MI heart in rats
Purpose: Acupuncture exerts cardioprotective effects on several types of cardiac injuries, especially myocardial ischemia (MI). In order to  elucidate the potential mechanisms,  RNA-seq by next generation sequencing was used to identify the rat genome-wide alterations after MI and EA treatment  in this study Methods: Adult male Sprague Dawley rats (250-300g)  were divided into three groups: Control, MI and electro-acupuncture (EA) groups, myocardium mRNA profiles of  rats in each group were generated by deep sequencing,using Illumina Hiseq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the mouse genome (UCSC RN4) and identified 121,233, 178,242, 161,880 transcripts in the Control, MI and EA rats  with TopHat and Cufflinks workflow respectively.  Approximately 32% and 22% of the transcripts showed differential expression between the Control and MI, MI and EA respectively with a fold change =2.0. Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat MI model and in acupuncture treatment by high throughput sequencing. The optimized data analysis workflows reported here should provide a framework for acupuncture investigations of expression profiles. Overall design: Myocardium mRNA profiles of  Control, MI and EA  rats were generated by Hiseq 2000, Control and MI+EA group there were three samples, MI group there were two samples.