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Sample GSM2973400 Query DataSets for GSM2973400
Status Public on Mar 13, 2018
Title Ishi_E2_ChIP_H3K27ac
Sample type SRA
 
Source name Ishikawa
Organism Homo sapiens
Characteristics cell line: Ishikawa
treatment: 10 nM Estradiol for 8 hours
target protein: H3K27ac
antibody: H3K27ac pAb (Active Motif 39133)
Treatment protocol Cells were treated with 100 nM dexamethasone, 10 nM 17-beta-estradiol, or vehicle control (DMSO) for 1 hour prior to crosslinking.
Growth protocol Ishikawa cells were grown in phenol red-free RPMI-1640 media supplemented with 10% charcoal/dextran treated fetal bovine serum and 50 units/mL penicillin and 50 µg/mL streptomycin for at least 4 days before treatment.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed in 1% formaldehyde for 10 minutes at room temperature and then treated with 125 mM Glycine for 5 minutes to stop crosslinking. Crosslinked cells were then washed with cold PBS and scraped to harvest.
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 with the following arguments: bowtie --chunkmbs 512 -m 1 -t --best -q -S -l 32 -e 80 -n 2
Peaks were called using macs2 V 2.1.0.20140616 with the following arguments: macs2 callpeak -B --SPMR --pvalue=1e-10 --mfold 15 100
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files, pileup values for reads
Supplementary_files_format_and_content: Excel file, Chromosome, start, stop, length, summit, pvalue, fold_enrichment, qvalue, and name values for peaks called by macs2
 
Submission date Jan 30, 2018
Last update date Mar 13, 2018
Contact name Jason Gertz
E-mail(s) jay.gertz@hci.utah.edu
Organization name University of Utah
Department Oncological Sciences
Lab Gertz
Street address 2000 Circle of Hope
City Salt Lake CIty
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL16791
Series (2)
GSE109891 Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer [ChIP-seq]
GSE109893 Clinical and genomic crosstalk between glucocorticoid receptor and estrogen receptor α in endometrial cancer
Relations
BioSample SAMN08439018
SRA SRX3630820

Supplementary file Size Download File type/resource
GSM2973400_H3K27ac_E2_8hr.bw 94.5 Mb (ftp)(http) BW
GSM2973400_H3K27ac_E2_8hr_peaks.txt.gz 741.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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