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Sample GSM451825 Query DataSets for GSM451825
Status Public on Sep 11, 2009
Title IgG_ChIA-PET (454)
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 454 GS FLX
 
Description A control ChIA-PET library against IgG (mock ChIP) in MCF-7 human breast cancer cells in estrogen-treated condition.
Data processing Mapping analysis was performed by Compressed Suffix Arrays 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
E-mail(s) ruanyj@gis.a-star.edu.sg
Phone 65 6478 8073
URL http://www.gis.a-star.edu.sg
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 GPL9186
Series (1)
GSE18046 An Estrogen Receptor α-bound Human Chromatin Interactome
Relations
SRA SRX016698
BioSample SAMN00008906

Supplementary file Size Download File type/resource
GSM451825_IHM062_PEAK.out.txt.gz 92 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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