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Sample GSM1523076 Query DataSets for GSM1523076
Status Public on Jul 15, 2015
Title p300-E2-siNCAPD3_ChIPSeq
Sample type SRA
 
Source name beast cancer cell line
Organism Homo sapiens
Characteristics cell line: MCF7
chip antibody: p300
antibody vendor/catalog#: SC-585, Santa Cruz Biotech
treatment: cells transfected with siNCAPD3, and 1hr with 100nM E2, double crosslinked
Treatment protocol Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.
Growth protocol MCF7 obtained from ATCC were cultured in α-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.
Extracted molecule genomic DNA
Extraction protocol Lysates were crosslinked with 1% of formaldehyde or double-crosslinked with DSG first followed by 1% of formaldehyde, clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description cells transfected with siNCAPD3, and 1hr treatment with 100nM E2, double crosslinked, p300 ChIPseq was then performed.
Data processing Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
 
Submission date Oct 09, 2014
Last update date May 15, 2019
Contact name Qi Ma
E-mail(s) [email protected]
Organization name UCSD
Street address 9500 Gilman Dr,
City San Diego
ZIP/Postal code 92093
Country USA
 
Platform ID GPL11154
Series (2)
GSE62222 Interphase condensins regulate ligand-depedent enhancer activation (ChIP-seq)
GSE62229 Interphase condensins regulate ligand-depedent enhancer activation
Relations
BioSample SAMN03103617
SRA SRX730445

Supplementary file Size Download File type/resource
GSM1523076_Chipseq-P300-NCAPD3-MCF7-E2.bigWig 262.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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