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Status |
Public on Dec 27, 2019 |
Title |
H3K9m3_CD3_U1 |
Sample type |
SRA |
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Source name |
CD3+ LPMC
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Organism |
Homo sapiens |
Characteristics |
cell type: CD3+ LPMC strain: UC chip antibody: H3K9m3 (Abcam, clone ab8898)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Isolated cells were immediately cross-linked with 1% formaldehyde/PBS for 10 minutes at room temperature. After washing, the cell pellet was lysed in the lysis buffer having the following final concentration: 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1x proteinase inhibitor complete cocktail (Roche). The lysed solution was subjected to chromatin shearing by using Covaris S2 System (Covaris, Woburn, MA) to shear the chromatin into 100300 bp fragments. ChIP-seq libraries were prepared for sequencing using the SOLiD Fragment Library Construction Kit and multiplexed by using SOLiD™ Fragment Library Barcoding Kit Module 1-16 according to the manufacturer’s instructions.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
AB SOLiD 4 System |
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Data processing |
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.1 with default. peaks were called using MACS version 2.0.9 with default. Genome_build: hg19 Supplementary_files_format_and_content: wig files were generated using https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py;
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Submission date |
Mar 25, 2015 |
Last update date |
Dec 27, 2019 |
Contact name |
noriko nishi |
Organization name |
Axiohelix Co. Ltd.
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Street address |
5-11 hakozaki 5F Yunibasaru Bldg
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City |
tyuo-ku |
State/province |
Tokyo |
ZIP/Postal code |
103-0015 |
Country |
Japan |
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Platform ID |
GPL13393 |
Series (1) |
GSE67273 |
Genome-wide maps of chromatin state in immune cells derived from IBD patients |
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Relations |
BioSample |
SAMN03453555 |
SRA |
SRX974469 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1643566_H13.wig.gz |
28.3 Mb |
(ftp)(http) |
WIG |
GSM1643566_H13_peak.bed.gz |
24.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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