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Sample GSM1586010 Query DataSets for GSM1586010
Status Public on Jan 15, 2016
Title GCT27 - Embryocarcinoma cell line
Sample type genomic
 
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 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

Data table header descriptions
ID_REF
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00254956 0.8570952 0
cg22803477 0.845733 0
cg12639866 0.9109242 0
cg15092772 0.876921 0
cg26433816 0.6832061 0
cg01097325 0.8288719 0
cg04505750 0.6544489 0
cg19620994 0.8446943 0
cg22455725 0.8582974 0
cg22673583 0.2594423 0
cg06751920 0.8361813 0
cg11157076 0.8709677 0
cg09518518 0.8864437 0
cg01040782 0.8704293 0
cg20746830 0.8526276 0
cg04592706 0.8583138 0
cg09168805 0.6973112 0
cg04350215 0.8723449 0
cg04491808 0.6846284 0
cg12085314 0.1182997 0

Total number of rows: 313823

Table truncated, full table size 7073 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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