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| Status |
Public on Sep 05, 2018 |
| Title |
C3_methylation |
| Sample type |
SRA |
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| Source name |
Bull calf ID: 3 TRT: CL
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| Organism |
Bos taurus |
| Characteristics |
tissue: Liver
breed: Holstein
animal id: Bull calf ID: 3
treatment: CL
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from liver and mammary gland samples for reduced representation bisulfite sequencing analysis. Extraction, library construction, bisulfite treatment and sequencing were performed by Epigentek. DNA was isolated from 50 mg of tissue with the FitAmpTM General Tissue Section DNA Isolation Kit.
DNA was digested with MspI restriction enzyme for 2 hrs at 37°C followed by digestion with TaqαI restriction endonuclease at 65°C. DNA fragments < 300 bp were selected and used for bisulfite treatment with the Methylamp DNA Conversion Kit. Standard lllumina sequencing adaptors were ligated onto the bisulfite treated DNA fragments using a random probing method. Library amplification was achieved using indexed primers and analyzed on a Bioanalyzer and with a KAPA Library Quantification Kit according to the manufacturer’s protocol. Purified DNA (15 nM of sample) libraries were sequenced using the Illumina HiSeq 4000 system generating 50 bp single-end reads.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 4000 |
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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 reference genome (UMD3.1) using the software package Bismark (version: 0.17.0).
Methylation calls were performed for the alignment files using Bismark methylation extractor.
Genome_build: Cow genome assembly: UMD3.1
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 |
Sep 04, 2018 |
| Last update date |
Sep 05, 2018 |
| Contact name |
Francisco Peñagaricano |
| E-mail(s) |
fpenagarican@wisc.edu
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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 |
GPL23295 |
| Series (1) |
| GSE119445 |
In utero heat stress alters the offspring epigenome [methylation] |
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| Relations |
| BioSample |
SAMN09951480 |
| SRA |
SRX4638749 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3374744_C3.counts.txt.gz |
5.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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