|
| Status |
Public on Oct 10, 2013 |
| Title |
mTumor4vWTmsn_DAMD |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Eµ-MYC Tumor 4 DAMD Assay
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: Eµ-MYC Burkitt lymphoma tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell lines, primary human medulloblastoma, normal cerebellum, and mouse tumors using a QIAGEN Blood & Cell Culture DNA kit per manufacturer's instructions. The DAMD assay was performed as described (Mahoney SE, Yao Z, Keyes CC, Tapscott SJ, & Diede SJ (2012). Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics 7(4)).
|
| Label |
biotin
|
| Label protocol |
Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.
|
| |
|
| Channel 2 |
| Source name |
WTmsn DAMD Assay
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: normal mesenteric lymph node
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell lines, primary human medulloblastoma, normal cerebellum, and mouse tumors using a QIAGEN Blood & Cell Culture DNA kit per manufacturer's instructions. The DAMD assay was performed as described (Mahoney SE, Yao Z, Keyes CC, Tapscott SJ, & Diede SJ (2012). Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas. Epigenetics 7(4)).
|
| Label |
biotin
|
| Label protocol |
Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.
|
| |
|
| |
| Hybridization protocol |
Approximately 7.5μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
test CEL: mTumor4_rep1.CEL
test CEL: mTumor4_rep2.CEL
control CEL: mWTmsn_rep1.CEL
control CEL: mWTmsn_rep2.CEL
Eµ-MYC Tumor 4 DAMD, Technical Rep 1-2, Promoter Array
|
| Data processing |
Affymetrix Human or Mouse Tiling 1.0R Promoter Arrays were analyzed using Tiling Array Software (v 1.1.02, Affymetrix). Raw data were scaled to a target intensity of 100 and normalized by quantile normalization. For probe analysis, a bandwidth of 250 bp was used and perfect match (PM) probes were used in a Wilcoxon Rank Sum two-sided test.
|
| |
|
| Submission date |
Mar 18, 2013 |
| Last update date |
Oct 10, 2013 |
| Contact name |
Scott J. Diede |
| E-mail(s) |
scott.diede@merck.com
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Street address |
1100 Fairview Avenue North, Mailstop c3-168
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL5811 |
| Series (2) |
| GSE45240 |
Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer [Methylation profiling by array] |
| GSE45342 |
Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer |
|
