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Sample GSM2432888 Query DataSets for GSM2432888
Status Public on Apr 01, 2017
Title Pediatric brain tumor 1 - FF
Sample type genomic
 
Source name Pediatric brain tumor 1 - FF
Organism Homo sapiens
Characteristics tissue: brain tumor
Extracted molecule genomic DNA
Extraction protocol DNA from FF tumours was extracted with the DNeasy Blood & Tissue Kit (69504, Qiagen, Hilden, Germany) according to the manufacturer’s instructions with the addition of lysing the samples with the QIAGEN TissueLyser. FFPE samples (1-3 years old) were sectioned and DNA was isolated using QIAamp DNA FFPE Tissue Kit (56404, Qiagen) according to manufacturer’s recommendations except de-waxing steps with Xylene was repeated twice and the tissue was digested overnight. DNA concentration was determined with the Qubit® Fluorometer (Life technologies). The quality of the DNA extracted from FFPE samples was assessed in triplicates with the real-time PCR-based Illumina FFPE QC kit (WG-321-1001, Illumina, Inc., San Diego, CA) according to the provided protocol.
Label Cy5 and Cy3
Label protocol 500 ng FF DNA, 1 µg REPLI-g restored FFPE DNA and 1 µg unrestored FFPE DNA (for restoration with the Infinium kit after bisulfite conversion) was used for bisulfite conversion with the EZ DNA methylation kit (D5001, Zymo Research, Orange, CA) according to the manufacturer’s instructions using the alternative incubation conditions recommended for the Illumina Infinium methylation arrays. Successful conversion was verified by control PCR reactions with a primer set specific for bisulfite converted DNA and a primer set for unconverted DNA.
 
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchips using standard Illumina protocol
Scan protocol standard Illumina protocol
Data processing Raw methylation data was normalized using ssNoob-normalization with the R minfi package. CpG-sites with detection p-value >0.01 were regarded as failed and were assigned as missing.
 
Submission date Dec 19, 2016
Last update date Apr 01, 2017
Contact name Helena Carén
Organization name Gothenburg University
Street address Medicinaregatan 1F
City Gothenburg
ZIP/Postal code 413 90
Country Sweden
 
Platform ID GPL21145
Series (2)
GSE92579 Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours (EPIC)
GSE92580 Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours

Data table header descriptions
ID_REF
VALUE ssNoob-normalization
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg18478105 0.0125539156767525 0
cg09835024 0.0303067012842871 0
cg14361672 0.854467289230365 0
cg01763666 0.828776998041936 0
cg12950382 0.879704886839481 0
cg02115394 0.0209785651295992 0
cg25813447 0.0404129204050589 0
cg07779434 0.0561330838701386 0
cg13417420 0.0138271224331126 0
cg12480843 0.0173718353285881 0
cg26724186 0.95999668906517 0
cg24133276 0.0158195940415097 0
cg00617867 0.970648671980933 0
cg13773083 0.048467132855432 0
cg17236668 0.903396993762599 0
cg19607165 0.0209178050921733 0
cg11073926 0.0171860593429975 0
cg08770523 0.0206636566886803 0
cg08795713 0.808064220793447 0
cg24040570 0.013942478987177 0

Total number of rows: 866836

Table truncated, full table size 26430 Kbytes.




Supplementary file Size Download File type/resource
GSM2432888_200772300032_R01C01_Grn.idat.gz 7.0 Mb (ftp)(http) IDAT
GSM2432888_200772300032_R01C01_Red.idat.gz 7.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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