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Sample GSM5534975 Query DataSets for GSM5534975
Status Public on Aug 25, 2021
Title Human Ependymoma Tissue [EPEND311]
Sample type genomic
 
Source name Human Ependymoma Tissue
Organism Homo sapiens
Characteristics tissue: Ependymoma
methylation class: PFA
classifier score: 1
who grade: III
tumour location: PF
event free survival: 183
overall survival: 183
survival status: A
recurrence: No
1q gain: no gain
resection status: ISR
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 EPEND311
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 0.788659794 0
cg14008030 0.505688906 0
cg12045430 0.229027176 0
cg20826792 0.168293718 0
cg00381604 0.054596888 0
cg20253340 0.418095281 0
cg21870274 0.805354099 0
cg24335620 0.803557114 0
cg16162899 0.79230416 7.59E-104
cg17149495 0.528173375 1.01E-208
cg22802167 0.967452301 0
cg24669183 0.72078477 0
cg17308840 0.636323713 7.13E-218
cg17866181 0.893441951 0
cg24159721 0.120131164 0
cg15174812 0.102228305 0
cg08477687 0.266030747 1.59E-219
cg00034556 0.140659434 0
cg00645010 0.101854441 0
cg15394630 0.15299127 0

Total number of rows: 438007

Table truncated, full table size 11427 Kbytes.




Supplementary file Size Download File type/resource
GSM5534975_200069280174_R05C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM5534975_200069280174_R05C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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