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Sample GSM381565 Query DataSets for GSM381565
Status Public on Mar 18, 2009
Title TGCT_Methylation_hg17_Chip_5
Sample type genomic
 
Channel 1
Source name MeDIP DNA from cultured testicular cancer cells
Organism Homo sapiens
Characteristics cell line: Ntera2
gender: male
tissue: testis
antibody: mouse anti-5-methylcytidine monoclonal antibody
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from cultured cells using Gentra Puregene Kit (Qiagen) and then sonicated on ice to give random fragments of 100-500 bp.
Label biotin
Label protocol Amplified DNA samples (9 μg) were enzymatically fragmented and biotin-labeled using the WT Labeling Kit (Affymetrix).
 
Channel 2
Source name MeDIP DNA from cultured normal testis cells
Organism Homo sapiens
Characteristics cell line: CRL-7002
gender: male
tissue: testis
antibody: mouse anti-5-methylcytidine monoclonal antibody
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from cultured cells using Gentra Puregene Kit (Qiagen) and then sonicated on ice to give random fragments of 100-500 bp.
Label biotin
Label protocol Amplified DNA samples (9 μg) were enzymatically fragmented and biotin-labeled using the WT Labeling Kit (Affymetrix).
 
 
Hybridization protocol Biotin-labeled DNA was hybridized to each array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The hybridization mix was removed from these arrays and reused to hybridize the remaining arrays. Hybridized arrays were washed and stained on the Affymetrix Fluidic Station 450.
Scan protocol Arrays were scanned on an Affymetrix GeneChip Scanner GCS3000 7G.
Description TGCT MeDIP-chip technical replicates 1-3, Chip E
Data processing CEL files from tiling arrays were analyzed by Tiling Analysis Software (TAS). Arrays from each group (cancer vs normal) were quantile-normalized and differential methylation between groups of tumor and normal was compared by choosing the “two-sample comparison analysis” option in TAS. A two-sided test was performed to evaluate both hypermethylation and hypomethylation. Transfrags (or DMRs) were generated by Interval Analysis with a p-value cutoff at 20 (p < 0.01) and a bandwidth of 275. Transfrags generated by p-value cutoff with a positive signal difference were defined as hypermethylation while those of negative difference were defined as hypomethylation.

signal.bar files store the signal comparison between normal and tumor cells. Pvalue.bar files store the p-value (-10log10) of each probe. NT2-IP CEL files correspond to Ntera2 DNA hybridizations, and HT-IP CEL files correspond to CRL-7002 DNA hybridizations.
 
Submission date Mar 17, 2009
Last update date Mar 17, 2009
Contact name Hoi Hung Cheung
E-mail(s) cheungho@mail.nih.gov
Phone 301-451-8368
Organization name NICHD
Lab Laboratory of Clinical and Developmental Genomics
Street address 49 Convent Dr, Rm.2C08 Bldg.49
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4914
Series (1)
GSE15220 Genome-wide analysis of differential methylation and gene expression in a testicular cancer cell line

Supplementary file Size Download File type/resource
GSM381565_E-2-samples-analysis_pvalue.bar.gz 34.5 Mb (ftp)(http) BAR
GSM381565_E-2-samples-analysis_signal.bar.gz 34.8 Mb (ftp)(http) BAR
GSM381565_HT-IP1-E4.CEL.gz 22.7 Mb (ftp)(http) CEL
GSM381565_HT-IP2-E4.CEL.gz 22.3 Mb (ftp)(http) CEL
GSM381565_HT-IP3-E4.CEL.gz 23.3 Mb (ftp)(http) CEL
GSM381565_NT2-IP1-E4.CEL.gz 22.7 Mb (ftp)(http) CEL
GSM381565_NT2-IP2-E4.CEL.gz 23.1 Mb (ftp)(http) CEL
GSM381565_NT2-IP3-E4.CEL.gz 22.7 Mb (ftp)(http) CEL
Processed data are available on Series record
Processed data provided as supplementary file

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