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| Status |
Public on Jan 24, 2014 |
| Title |
Histone H3 |
| Sample type |
SRA |
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| Source name |
MDBK cell, normal, Histone H3
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| Organism |
Bos taurus |
| Characteristics |
cell line: MDBK
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with 10 mM butyrate for 24 hr, The cells were scraped from the flask and homogenized with ice-cold Dounce homogenizer to release the nuclei. The collected nuclei were resuspended in digestion buffer and enzymatic shearing was performed. ChIP with anti H3, H4 and acetyl-H3 and H4.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
For enriched-region (peaks) identification, we used the MACS (Model-based Analysis of ChIP-seq) algorithm for peak detection
Using MACS version 1.4 (Orc2, 20110214) and ARGUMENTS settings as band width =200; model fold = 10, 30; P value cutoff = 1.00e-05 range for calculating regional lambda is 10,000 bps.
Genome_build: bosTau4
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| Submission date |
Jun 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Congjun Li |
| E-mail(s) |
congjun.li@ars.usda.gov
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| Organization name |
ARS, USDA
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| Department |
BFGL
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| Street address |
10300 Baltimore Ave
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| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
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| Platform ID |
GPL15750 |
| Series (1) |
| GSE38973 |
ChIP-seq of bovine cells (MDBK) to study butyrate-induced histone modification |
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| Relations |
| SRA |
SRX156364 |
| BioSample |
SAMN01081736 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM953084_macs_out_anti_H3_bosTau4.map_MACS_wiggle.tar.gz |
259.9 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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