|
| Status |
Public on Jan 15, 2016 |
| Title |
GCT44 - Yolk Sac Tumour cell line |
| Sample type |
genomic |
| |
|
| Source name |
Yolk Sac Tumour (Roach, 1994)
|
| Organism |
Homo sapiens |
| Characteristics |
histological_subtype_primary tumor: Yolk Sac Tumour
anatomical localisation: human testicular GCT
cell line: GCT44
|
| Growth protocol |
Cell lines were cultured in Dulbecco’s Modified Eagle Medium (EC, Teratoma and YST) and RPMI-1640 media (Seminoma) (Sigma-Aldrich). containing 10% fetal bovine serum (Sigma-Aldrich). and 1% Penicillin/Streptomycin (Sigma-Aldrich).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulphite conversion of the DNA (1µg) was performed using EZ DNA methylation kit (Zymo),
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Illumina Infinium HD Assay Methylation Protocol using the HumanMethylation450 BeadChip.
|
| |
|
| Hybridization protocol |
hybridization to the Infinium HumanMethylome450 arrays (Illumina) performed by the Queen Mary University of London Genome Centre, using the Illumina Infinium HD Assay Methylation Protocol.
|
| Scan protocol |
Illumina iScan with Autoloader2 to scan the arrays, and data has been analysed using the Illumina GenomeStudio Methylation Module v1.9 performed by the Queen Mary University of London Genome Centre.
|
| Data processing |
The Excel tool PivotTable was used to assign average methylation and differential methylation measurements to each gene according to various combinations of locations with respect to CpG islands and gene regions. Probes labelled by multiple gene names were excluded from the analysis. Unmethylated and methylated signal intensities are available on the series record.
|
| |
|
| Submission date |
Jan 15, 2015 |
| Last update date |
Jan 15, 2016 |
| Contact name |
Paul J Scotting |
| Organization name |
University of Nottingham
|
| Department |
School of Life Sciences
|
| Lab |
D13
|
| Street address |
Queen's Medical Centre
|
| City |
Nottingham |
| ZIP/Postal code |
NG7 2UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE65027 |
Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [methylation] |
| GSE65028 |
Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines |
|
