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Sample GSM5534973 Query DataSets for GSM5534973
Status Public on Aug 25, 2021
Title Human Ependymoma Tissue [EPEND019]
Sample type genomic
 
Source name Human Ependymoma Tissue
Organism Homo sapiens
Characteristics tissue: Ependymoma
methylation class: PFA
classifier score: 0.98
who grade: II
tumour location: PF
event free survival: 30
overall survival: 67
survival status: D
recurrence: Yes
1q gain: gain
resection status: CSR
Extracted molecule genomic DNA
Extraction protocol DNA extracted from formalin fixed, paraffin embedded material using the Qiagen ALLprep kit as per protocol.
Label biotin/dnp
Label protocol Illumina Protocol
 
Hybridization protocol Illumina Protocol
Scan protocol Illumina Protocol
Description EPEND019
Data processing Bioconductor (version 3.3) package minifi (version 1.18) using function preprocessIllumina. Data filtered for SNPs, sex chromosomes and probes with detection p-value>0.01.
 
Submission date Aug 24, 2021
Last update date Sep 14, 2023
Contact name Timothy A Ritzmann
E-mail(s) Timothy.ritzmann@nhs.net
Organization name University of Nottingham
Department Children's Brain Tumour Research Centre
Street address Coates Road
City Nottingham
ZIP/Postal code NG7 2UH
Country United Kingdom
 
Platform ID GPL13534
Series (1)
GSE182707 DNA methylation profiles for the SIOP Ependymoma I Study
Relations
Reanalyzed by GSE243240

Data table header descriptions
ID_REF
VALUE Beta values extracted following the minfi preprocessIllumina function.
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg13869341 0.877178308 0
cg14008030 0.770593065 0
cg12045430 0.279844031 0
cg20826792 0.326563467 0
cg00381604 0.120348205 0
cg20253340 0.68189582 0
cg21870274 0.840512996 0
cg24335620 0.855478126 0
cg16162899 0.878706561 1.75E-13
cg17149495 0.364665354 9.90E-154
cg22802167 0.928882175 0
cg24669183 0.828698881 0
cg17308840 0.88359647 1.28E-203
cg17866181 0.790025732 1.24E-64
cg24159721 0.114168538 0
cg15174812 0.124648082 0
cg08477687 0.106193259 0
cg00034556 0.126458006 0
cg00645010 0.095459353 0
cg15394630 0.131607582 0

Total number of rows: 438007

Table truncated, full table size 12422 Kbytes.




Supplementary file Size Download File type/resource
GSM5534973_200078650079_R04C02_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM5534973_200078650079_R04C02_Red.idat.gz 3.9 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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