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Sample GSM451985 Query DataSets for GSM451985
Status Public on Sep 11, 2009
Title ERα_ChIA-PET_Replicate1 (Illumina)
Sample type SRA
Source name MCF-7 cells
Organism Homo sapiens
Characteristics library: ChIA-PET
Treatment protocol In preparation for the 17 beta-estradiol (“estrogen”, E2, Sigma) treatment, cells were grown in hormone-free media: they were washed with PBS and incubated in phenol red-free medium (Invitrogen/Gibco) supplemented with 5% charcoal-dextran stripped FBS (Hyclone), penicillin, streptomycin, gentamycin, and L-glutamine (Invitrogen) for a minimum of 72 hours. Hormone-depleted cells were treated with estrogen to a final concentration of 100 nM for 45 min before the ChIP procedure.
Growth protocol MCF-7 cells were grown to at least 80% confluence in DMEM/F12 (Invitrogen/Gibco) supplemented with 5% FBS (Invitrogen/Gibco), penicillin (Invitrogen), streptomycin (Invitrogen), and gentamycin (Invitrogen).
Extracted molecule genomic DNA
Extraction protocol We used 1% formaldehyde to crosslink the cells, and sonication to break the chromatin fibers. Antibodies were used to enrich chromatin fragments by ChIP. After this either ChIA-PET or ChIP-Seq was performed.
Library strategy ChIA-PET
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description 1 biological replicate of a ChIA-PET library against ERα in MCF-7 human breast cancer cells in estrogen-treated condition.
Data processing Mapping analysis was performed by ELAND and results were further processed using the ChIA-PET pipeline software.
Submission date Sep 11, 2009
Last update date May 15, 2019
Contact name Yijun Ruan
Phone 65 6478 8073
Organization name Genome Institute of Singapore
Department Research Computing Group
Street address 60 Biopolis Street, #02-01 Genome, Singapore 138672
City Singapore
State/province Singapore
ZIP/Postal code 138672
Country Singapore
Platform ID GPL9052
Series (1)
GSE18046 An Estrogen Receptor α-bound Human Chromatin Interactome
SRA SRX016699
BioSample SAMN00008907

Supplementary file Size Download File type/resource
GSM451985_IHM001F_PEAK.out.txt.gz 128.3 Kb (ftp)(http) TXT
GSM451985_IHM001H_PEAK.out.txt.gz 31.0 Kb (ftp)(http) TXT
GSM451985_IHM001_HNV3_PEAK.out.txt.gz 1.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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