|
| Status |
Public on Jan 20, 2009 |
| Title |
H3K4me2 patterns in DKO |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DKO Immunoprecipitated DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Immunoprecipitation using a specific antibody for H3K4me2 of the DKO human colorectal cancer cell line
|
| Biomaterial provider |
Bert Vogelstein
|
| Treatment protocol |
ChIP DNA using a H3K4me2 specific antibody
|
| Growth protocol |
McCoy’s 5A modified medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Multiple phenol:chloroform:isoamyl alcohol extractions
|
| Label |
Cy5
|
| Label protocol |
Bioprime random primer labeling kits
|
| |
|
| Channel 2 |
| Source name |
DKO WCE
|
| Organism |
Homo sapiens |
| Characteristics |
Whole cell extract of the DKO human colorectal cancer cell line
|
| Biomaterial provider |
Bert Vogelstein
|
| Treatment protocol |
Whole cell extract
|
| Growth protocol |
McCoy’s 5A modified medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Multiple phenol:chloroform:isoamyl alcohol extractions
|
| Label |
Cy3
|
| Label protocol |
Bioprime random primer labeling kits
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was mixed (5 – 6 µg each of immunoenriched and whole cell extract DNA) and hybridized to arrays in Agilent hybridization chambers for 20 hours at 40°C.
|
| Scan protocol |
Hybridized microarrays were scanned using an Agilent G2565BA microarray scanner.
|
| Description |
none
|
| Data processing |
Median blanks subtraction followed by an inter-array median normalization and a dye-bias median normalization. Downstream analysis in R.
|
| |
|
| Submission date |
Apr 15, 2008 |
| Last update date |
Jan 20, 2009 |
| Contact name |
Leander Van Neste |
| Organization name |
Ghent University
|
| Department |
Molecular Biotechnology
|
| Lab |
Bioinformatics and Computational Genomics
|
| Street address |
Coupure Links 653
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL4125 |
| Series (1) |
| GSE11173 |
Defining a Chromatin Pattern That Characterizes DNA Hypermethylated Genes in Colon Cancer Cells |
|
