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Status |
Public on Mar 16, 2009 |
Title |
Input Samples for MCF7 Cells (Whole Genome # 6, Replicate # 1) |
Sample type |
genomic |
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Source name |
Chromatin Immunoprecipitated DNA
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Organism |
Homo sapiens |
Characteristics |
cell type: MCF7 cells
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Treatment protocol |
MCF7 Cells were hormone-deprived for 3 days and then were treated with nuclear receptor ligand or vehicle at 80% confluence.
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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.
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Extracted molecule |
genomic DNA |
Extraction protocol |
According to the standard chromatin extraction protocol (Shang et al., 2000).
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Label |
biotin
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Label protocol |
ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.
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Hybridization protocol |
According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).
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Scan protocol |
According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).
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Description |
Input DNA from MCF-7 cells hybridized on Affymetrix whole genome tiling arrays 2.0R.
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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.
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Submission date |
Mar 16, 2009 |
Last update date |
Mar 16, 2009 |
Contact name |
Sujun Hua |
E-mail(s) |
shua@mdanderson.org
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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 |
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Platform ID |
GPL4915 |
Series (1) |
GSE15244 |
Genome-wide Binding Site Mapping of Retinoic Acid Receptors and Coregulators in Breast Cancer Cells |
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