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| Status |
Public on Sep 18, 2012 |
| Title |
AABB_PolII_ChIP-seq |
| Sample type |
SRA |
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| Source name |
Mammary tissues
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: RNA polymerase II
antibody vendor/catalog#: Abcam, ab5408
strain: 129SV::FVB/N::C57BL/6
developmental stage: Day of parturition
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen-stored mammary tissues were broken into powder with mortar and pestle and then cross-linked with 1% formaldehyde for 10 min, and their nuclei were fractionated by sucrose density gradient centrifugation. Chromatin was fragmented to 200 to 300 bp by sonication. Antibodies against STAT5A (# sc-1081, Santa Cruz, CA), STAT5B (# sc-835, Santa Cruz), RNA polymerase II (# ab5408, Abcam), and histone H3K4me3 (# 17-614, Millipore, Temecula, CA) were used for ChIP.
The ChIP DNA fragments were blunt-ended and ligated to the Illumina Indexed DNA adaptors using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (# E6240, New England BioLabs, Ipswich, MA), and sequenced using the Illumina HiSeq 2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the BWA program (Li et al, Bioinformatics)
Peaks were called using HOMER with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and bed files generated by HOMER
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| Submission date |
Sep 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Keunsoo Kang |
| E-mail(s) |
[email protected]
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| Phone |
82-41-550-3456
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| Organization name |
Dankook University
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| Department |
Microbiology
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| Lab |
Computational Biology Lab
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| Street address |
Dandae-ro 119
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| City |
Cheonan |
| State/province |
Chungnam |
| ZIP/Postal code |
31116 |
| Country |
South Korea |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE40930 |
Impact of STAT5 dosage and binding location on genetic and biological programs activated in mouse mammary epithelium during pregnancy. |
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| Relations |
| SRA |
SRX187510 |
| BioSample |
SAMN01178428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1005191_L1-AABB-PolII.ucsc.bedGraph.gz |
94.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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