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Sample GSM1643566 Query DataSets for GSM1643566
Status Public on Dec 27, 2019
Title H3K9m3_CD3_U1
Sample type SRA
 
Source name CD3+ LPMC
Organism Homo sapiens
Characteristics cell type: CD3+ LPMC
strain: UC
chip antibody: H3K9m3 (Abcam, clone ab8898)
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model AB SOLiD 4 System
 
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;
 
Submission date Mar 25, 2015
Last update date Dec 27, 2019
Contact name noriko nishi
Organization name Axiohelix Co. Ltd.
Street address 5-11 hakozaki 5F Yunibasaru Bldg
City tyuo-ku
State/province Tokyo
ZIP/Postal code 103-0015
Country Japan
 
Platform ID GPL13393
Series (1)
GSE67273 Genome-wide maps of chromatin state in immune cells derived from IBD patients
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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