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| Status |
Public on Sep 29, 2023 |
| Title |
MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity |
| Organism |
Sus scrofa |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
We report the application of methylated DNA immunopreciptation (MeDIP)-next generation sequencing for examining methylome in two different breeds of pigs. Two muscle samples from each animal/breed processed to isolated DNA. DNA was isolated from two muscle samples (one per breed) was used for methylated DNA immunoprecipitation (MeDIP). 5 methyl cytosine regions were immunoprecipitated and processed for next generation sequencing in Hiseq 2500 (Illumina). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment (BWA) (version 0.7.17). The MeDIP data generated was used for identification of differentially methylated regions (DMRs) across the chromosome between the breeds using Burrrows Eheeler Alignment (BWA version 0.7.17. Uniquely mapped reads were processed further with MEDIPS. A total of 1545 and 25 DMRs (P<0.1) were identified across the pig chromosome and mitochondrial DNA respectively.
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| Overall design |
Methylome analysis of muscle from two pig breeds with varying muscularity was conducted to provide insights into muscle development.
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| Contributor(s) |
Mohan NH, Pathak P, Buragohain L, Deka J, Das AK, Thomas R, Singh R, Bharati J, Sarma DK, Gupta VK, Das BC |
| Citation missing |
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| Submission date |
Sep 29, 2021 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Narayana H Mohan |
| E-mail(s) |
mohan.nh@icar.gov.in
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| Organization name |
Indian Council of Agricultural Research
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| Department |
ICAR-National Research Centre on Pig
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| Lab |
Physiology laboratory
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| Street address |
Rani
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| City |
Guwahati |
| State/province |
Assam |
| ZIP/Postal code |
781 131 |
| Country |
India |
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| Platforms (1) |
| GPL19176 |
Illumina HiSeq 2500 (Sus scrofa) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE184970 |
Muscle from two pig breeds with varying muscularity |
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| Relations |
| BioProject |
PRJNA767248 |
| SRA |
SRP339248 |
