|
| Status |
Public on Jan 01, 2013 |
| Title |
FAIRE-array6 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
FAIRE ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7 cells
chromatin mark: FAIRE
antibody vendor: NA
antibody catalog #: NA
|
| Treatment protocol |
MCF7 Cells were grown in growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), until 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.
|
| 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 (see Sujun et al, 2009).
|
| 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: MCF7 cells
|
| Treatment protocol |
MCF7 Cells were grown in growing in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), until 80% confluence. ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.
|
| 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 (see Sujun et al, 2009).
|
| 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 |
control CEL files: input1-6.CEL, input2-6.CEL, input3-6.CEL
FAIRE 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.
results file descriptions: Bed files for enriched ChIP sites of each of 6 chromatins marks.
|
| |
|
| Submission date |
Nov 29, 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) |
| GSE42617 |
ChIP-chip of 6 chromatin marks (FAIRE, H3K4me1, H3K4me3, H3K27me3, H3R17me2, H3AZAce) in breast cancer cell line MCF7 |
|
