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Sample GSM1099701 Query DataSets for GSM1099701
Status Public on Oct 10, 2013
Title Daudi_DAMD
Sample type genomic
 
Channel 1
Source name Daudi DAMD Assay
Organism Homo sapiens
Characteristics cell line: Daudi
cell type: Burkitt lymphoma cancer cell
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 WBC DAMD Assay
Organism Homo sapiens
Characteristics cell type: peripheral white blood cells
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 control CEL: hWBC_rep1.CEL
control CEL: hWBC_rep2.CEL
Daudi 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 GPL5082
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

Supplementary file Size Download File type/resource
GSM1099701_hDaudi_pvalue.bar.gz 23.0 Mb (ftp)(http) BAR
GSM1099701_hDaudi_rep1.CEL.gz 15.3 Mb (ftp)(http) CEL
GSM1099701_hDaudi_rep2.CEL.gz 15.0 Mb (ftp)(http) CEL
GSM1099701_hDaudi_signal.bar.gz 22.7 Mb (ftp)(http) BAR
Processed data provided as supplementary file

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