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| Status |
Public on Mar 20, 2016 |
| Title |
Genome-wide profiling of gene expression under electro-acupuncture pretreatment on myocardial I/R injury in rats |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose:Acupuncture exerts cardioprotective effect on myocardial I/R injury. In order to elucidate the potential mechanisms, RNA-seq by next generation sequencing was used to identify the rat genome-wide alterations by EA at Neiguan acupoint pretreatment in this study
Methods: Adult male Sprague Dawley rats (250-300g) were divided into four groups: Sham operation(SO), I/R, electro-acupuncture at Neiguan pretreatment (EA) and electro-acupuncture at non-acupoint (NA) groups and 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 20~43 million sequence reads per sample to the mouse genome (UCSC RN4) and identified 26190 22895 25160 22852 transcripts in the SO, I/R, EA and NA rats with TopHat and Cufflinks workflow respectively. Approximately 32% and 22% of the transcripts showed differential expression between the SO and I/R, I/R and EA , I/R and NA, respectively with a |log2 fold change |≥1.
Conclusions: Our results for the first time generated genome-wide gene expression profiles both in the rat I/R 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.
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| Overall design |
Myocardium mRNA profiles of SO, I/R, EA and NA rats were generated by Hiseq 2000, Each group there were two samples.
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| Contributor(s) |
Zhu B, Huang Y, Hu C |
| Citation(s) |
25302705 |
| Submission date |
Sep 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing-Mei Zhu |
| E-mail(s) |
zhubm64@hotmail.com
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| Phone |
+86-025-85811235
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| Organization name |
Nanjing university of Chinese Medicine
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| Street address |
138 Xianlin Avenue
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210023 |
| Country |
China |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA262523 |
| SRA |
SRP048215 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61840_RAW.tar |
5.3 Mb |
(http)(custom) |
TAR (of FPKM_TRACKING) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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