|
| Status |
Public on Mar 18, 2009 |
| Title |
TGCT_Methylation_hg17_Chip_6 |
| 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 F
|
| 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 |
GPL4915 |
| Series (1) |
| GSE15220 |
Genome-wide analysis of differential methylation and gene expression in a testicular cancer cell line |
|
