|
| Status |
Public on Jan 15, 2016 |
| Title |
GCT27 - Embryocarcinoma cell line |
| Sample type |
RNA |
| |
|
| Source name |
Embryocarcinoma (Andrews, 1998)
|
| Organism |
Homo sapiens |
| Characteristics |
histological_subtype_primary tumor: Embryocarcinoma
anatomical localisation: human testicular GCT
cell line: GCT27
|
| 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 |
total RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy extraction kit (Qiagen) according to the manufacturer protocol. RNA was eluted with RNAse-free water.
|
| Label |
biotin
|
| Label protocol |
not provided
|
| |
|
| Hybridization protocol |
not provided
|
| Scan protocol |
not provided
|
| Data processing |
Data was first preprocessed using the statistical software, R with packages provide by www.bioconductor.org. Data was preprocessed using the RMA method [66] and filtered such that probes which gave expression outputs below control background probes (recorded in the GeneChip) for all four cell lines were excluded. Fold changes in expression between each probe of each cell lines relative to Seminoma were calculated, and annotation packages were used to assign gene information to each probe set. The data was exported as a .txt file in order to be read and analysed in Excel. The Excel tool PivotTable was used to assign average expression intensity values to each gene.
|
| |
|
| 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 |
GPL570 |
| Series (2) |
| GSE65026 |
Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [gene expression] |
| GSE65028 |
Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines |
|
