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| Status |
Public on Nov 17, 2022 |
| Title |
M10 [Bisulfite-Seq] |
| Sample type |
SRA |
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| Source name |
Loin muscle
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| Organism |
Bos taurus |
| Characteristics |
tissue: Loin muscle
breed: Brangus
treatment: maternal diet control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from muscle samples and DNA quality and quantity were tested using Nanodrop (OD260/OD280) and Qubit® 2.0.
Bisulfite treatment, library preparation and subsequent whole-genome sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
The quality of the sequencing reads was evaluated using FastQC software, and if necessary, sequencing reads were trimmed using the software Trim Galore (version: 0.4.4).
Reads were mapped to the lastest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version 0.20.1).
Duplicate alignments were removed using the tool deduplicate_bismark (version 0.20.1).
Methylation calling and extraction were performed using Bismark methylation extractor (version 0.20.1).
Assembly: Cow genome assembly: ARS-UCD1.2
Supplementary files format and content: Tab-delimited text files including chromosome, genomic start position, genomic end position, percentage of methylation at that position, number of Cs methylated, and number of Cs non-methylated
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| Submission date |
Nov 15, 2022 |
| Last update date |
Nov 17, 2022 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
[email protected]
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| Organization name |
University of Wisconsin-Madison
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| Department |
Animal and Dairy Sciences
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| Street address |
1675 Observatory Drive
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL21659 |
| Series (2) |
| GSE117195 |
Maternal methionine supplementation alters the epigenome of the offspring |
| GSE218011 |
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves |
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| Relations |
| BioSample |
SAMN31745111 |
| SRA |
SRX18277940 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6732582_M10.txt.gz |
329.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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