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Sample GSM1029823 Query DataSets for GSM1029823
Status Public on Jan 01, 2013
Title ATF1-array6
Sample type genomic
 
Channel 1
Source name ATF1 ChIP
Organism Homo sapiens
Characteristics cell type: transgenic MCF7
transcription factor: ATF1
tag: modified LAP (localization and affinity purification) tag containing GFP
chip antibody: Goat anti-GFP
Treatment protocol According to the standard chromatin extraction protocol (Shang et al., 2000).
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.
For each NR with known ligand, MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM NR ligand at 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine. For orphan NRs and NR-cofactors, no ligand was used and ChIP was performed with cells growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml).
Extracted molecule genomic DNA
Extraction protocol ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.
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.
 
Channel 2
Source name Input DNA
Organism Homo sapiens
Characteristics cell type: transgenic MCF7
Treatment protocol According to the standard chromatin extraction protocol (Shang et al., 2000).
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.
For each NR with known ligand, MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM NR ligand at 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine. For orphan NRs and NR-cofactors, no ligand was used and ChIP was performed with cells growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml).
Extracted molecule genomic DNA
Extraction protocol ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.
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 Ch2 input ctrl CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
ATF1 ChIP - Array 6
Data processing Tiling array data were normalized and analyzed as described (Hua et al, 2009). 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-3) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions. Peaks located in the BAC regions, overlaps with GFP peaks, and overlaps with repetitive regions in the genome are filtered.
 
Submission date Nov 01, 2012
Last update date Jan 01, 2013
Contact name Jie Zhou
E-mail(s) jiezhou@uchicago.edu
Phone 3123163491
Organization name University of Chicago IGSB
Street address 900 East 57th Street, KCBD 10100
City Chicago
State/province ILLINOIS
ZIP/Postal code 60637
Country USA
 
Platform ID GPL4915
Series (1)
GSE41995 ChIP-chip of 38 nuclear receptors and NR co-factors in breast cancer cell line MCF7

Supplementary file Size Download File type/resource
GSM1029823_ATF1_TileGroup6_pvalue.bar.gz 33.6 Mb (ftp)(http) BAR
GSM1029823_reATF1_1_6.CEL.gz 24.8 Mb (ftp)(http) CEL
GSM1029823_reATF1_2_6.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM1029823_reATF1_3_6.CEL.gz 26.3 Mb (ftp)(http) CEL
Processed data provided as supplementary file
Processed data are available on Series record

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