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| Status |
Public on Jul 17, 2018 |
| Title |
6415_METHIONINE (bisulfite-seq) |
| Sample type |
SRA |
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| Source name |
Longissimus dorsi
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| Organism |
Bos taurus |
| Characteristics |
breed: Brangus-Angus
ID: 6415
treatment: METHIONINE
tissue: Longissimus dorsi
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from the muscle tissue for whole genome bisulfite sequencing analysis. Extraction, library construction, bisulfite treatment and sequencing were performed by Novogene Bioinformatics Technology Co., Ltd (Beijin, China). DNA was tested for purity using Nanodrop (OD260/OD280), DNA degradation and RNA contamination through an agarose gel electrophoresis and was quantified through Qubit.
DNA was fragmented into 200-300bp strands through the use of Covaris S220. Terminal repairing, A-ligation and adapters ligation were performed to the resulting fragments. The resulting DNA library was treated with bisulfite with the use of the EZ DNA Methylation Gold Kit from Zymo Research. Library concentration was quantified twice, first with Quibit 2.0 and after diluting to 1ng/ul, it was re-quantified with qPCR.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
bisulfite converted genomic DNA
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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 latest bovine reference genome (ARS-UCD1.2) using the software package Bismark (version: 0.17.0).
Mapping sequencing reads: a maximum of 1 mismatch was allowed during seed alignment.
The tool deduplicate_bismark was used to remove duplicate alignments.
Methylation calls were performed for the alinment files with the use of Bismark methylation extractor.
Genome_build: Cow genome assembly: ARS-UCD1.2
Supplementary_files_format_and_content: Tab-delimited text files including chromosome name, genomic start position, genomic end position, percentage of methylation at that position, number of C bases that are methylated and number of C bases that are unmethylated
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| Submission date |
Jul 16, 2018 |
| Last update date |
Aug 21, 2019 |
| 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) |
| GSE117194 |
Maternal methionine supplementation alters the epigenome of the offspring [Bisulfite-Seq] |
| GSE117195 |
Maternal methionine supplementation alters the epigenome of the offspring |
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| Relations |
| BioSample |
SAMN09667097 |
| SRA |
SRX4396783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3273343_M6415.final.txt.gz |
320.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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