|
| Status |
Public on Jun 30, 2011 |
| Title |
AOM/DSS-induced colon tumor |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MeDIP of AOM/DSS-induced colon tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: A pool of two AOM/DSS-induced colon tumors
dna treatment: Sonicated and immunoprecipitated with anti-5-methyl cytidine antibody (Diagenode, Liége, Belgium)
strain: BALB/c
|
| Growth protocol |
A pool of two AOM/DSS-induced colon tumors in BALB/c mice and a pool of two normal colonic epithelial cell samples obtained from untreated BALB/c mice by the crypt isolation technique were used. Samples were stored at -80 ˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High molecular weight DNA was extracted by the phenol/chloroform method.
|
| Label |
Cy5
|
| Label protocol |
Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).
|
| |
|
| Channel 2 |
| Source name |
AOM/DSS-induced colon tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: A pool of two AOM/DSS-induced colon tumors
dna treatment: Sonicated
strain: BALB/c
|
| Growth protocol |
A pool of two AOM/DSS-induced colon tumors in BALB/c mice and a pool of two normal colonic epithelial cell samples obtained from untreated BALB/c mice by the crypt isolation technique were used. Samples were stored at -80 ˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High molecular weight DNA was extracted by the phenol/chloroform method.
|
| Label |
Cy3
|
| Label protocol |
Sonicated DNA was labelled using Agilent Genomic DNA Labeling Kit PLUS (5188-5309).
|
| |
|
| |
| Hybridization protocol |
Labelled DNA mixed with Cot-1 DNA and Agilent blocking solution was hybridized to arrays for 40 hours at 67C and 10rpm. Arrays were washed as per Agilent protocol.
|
| Scan protocol |
Arrays were washed and scanned immediately with Agilent microarray scanner G2565BA.
Images were quantified using Agilent Feature Extraction 9.1 Software.
|
| Description |
MeDIP-CGI microarray analysis of AOM/DSS-induced colon tumors
|
| Data processing |
Arrays were processed using Agilent Feature Extraction 9.1 software and normalized (background subtraction and interarray median normalization) using Agilent Chip Analytics 1.3 software.
|
| |
|
| Submission date |
Apr 14, 2010 |
| Last update date |
Jun 30, 2011 |
| Contact name |
Satoshi Yamashita |
| E-mail(s) |
syamashi@maebashi-it.ac.jp
|
| Organization name |
National Cancer Center Research Institute
|
| Street address |
Tsukiji 5-1-1
|
| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10324 |
| Series (1) |
| GSE21333 |
Genome-wide methylation analysis of AOM/DSS-induced colon tumors |
|
