Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide profiling of gene expression under electro-acupuncture treatment on MI heart in rats

ABSTRACT: 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: BurrowsâWheeler 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 â¥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. 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.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Bing-Mei Zhu

PROVIDER: E-GEOD-54132 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Acupuncture promotes angiogenesis after myocardial ischemia through H3K9 acetylation regulation at VEGF gene.

Fu Shu-Ping SP He Su-Yun SY Xu Bin B Hu Chen-Jun CJ Lu Sheng-Feng SF Shen Wei-Xing WX Huang Yan Y Hong Hao H Li Qian Q Wang Ning N Liu Xuan-Liang XL Liang Fanrong F Zhu Bing-Mei BM

PloS one 20140410 4

<h4>Background</h4>Acupuncture exerts cardioprotective effects on several types of cardiac injuries, especially myocardial ischemia (MI), but the mechanisms have not yet been well elucidated. Angiogenesis mediated by VEGF gene expression and its modification through histone acetylation has been considered a target in treating myocardial ischemia. This study aims to exam whether modulation of angiogenesis through H3K9 acetylation regulation at VEGF gene is one possible cardioprotective mechanism ...[more]

PMID: 24722278

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