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Sample GSM380699 Query DataSets for GSM380699
Status Public on Mar 16, 2009
Title Input Samples for MCF7 Cells (Whole Genome # 6, Replicate # 1)
Sample type genomic
 
Source name Chromatin Immunoprecipitated DNA
Organism Homo sapiens
Characteristics cell type: MCF7 cells
Treatment protocol MCF7 Cells were hormone-deprived for 3 days and then were treated with nuclear receptor ligand or vehicle at 80% confluence.
Growth protocol MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.
Extracted molecule genomic DNA
Extraction protocol According to the standard chromatin extraction protocol (Shang et al., 2000).
Label biotin
Label protocol ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.
 
Hybridization protocol According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).
Scan protocol According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).
Description Input DNA from MCF-7 cells hybridized on Affymetrix whole genome tiling arrays 2.0R.
Data processing Tiling array data were normalized and analyzed as described (Cawley et al, 2004). Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of +/-250 bp was generated. A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions. Significantly enriched probes (p < 1e-4) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.
 
Submission date Mar 16, 2009
Last update date Mar 16, 2009
Contact name Sujun Hua
E-mail(s) shua@mdanderson.org
Organization name MD Anderson Cancer Center
Lab Ronald DePinho Lab
Street address 1901 East Rd
City Houston
State/province Tx
ZIP/Postal code 77054
Country USA
 
Platform ID GPL4915
Series (1)
GSE15244 Genome-wide Binding Site Mapping of Retinoic Acid Receptors and Coregulators in Breast Cancer Cells

Supplementary file Size Download File type/resource
GSM380699.CEL.gz 22.5 Mb (ftp)(http) CEL
Processed data not provided for this record

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