|
Status |
Public on Oct 10, 2013 |
Title |
mTumor4vWTspleen_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 |
WTspleen DAMD Assay
|
Organism |
Mus musculus |
Characteristics |
background strain: C57BL/6 tissue: normal spleen
|
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: mWTspleen_rep1.CEL control CEL: mWTspleen_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.
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|
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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 |
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