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Sample GSM5732120 Query DataSets for GSM5732120
Status Public on Oct 02, 2023
Title Human Ependymoma Tissue (Epend03P)
Sample type genomic
 
Source name Human Ependymoma Tissue
Organism Homo sapiens
Characteristics disease state: pediatric ependymoma
methylation class: PF_EPN_A
gender: Male
who grade: 2
tumor location: PF
event free survival: 32
overall survival: 132
survival status: Alive
recurrence: recurrence
1q gain: gain
resection status: Complete
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
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 Dec 13, 2021
Last update date Oct 02, 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)
GSE190798 Retrospective DNA Methylation profiles collated from Nottingham, UK

Data table header descriptions
ID_REF
VALUE Beta values (minfi)
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
cg13869341 0.786815132 0
cg14008030 0.624544937 0
cg12045430 0.123573777 0
cg20826792 0.129732961 0
cg00381604 0.052482634 0
cg20253340 0.419561128 0
cg21870274 0.690296204 0
cg24335620 0.795079071 0
cg16162899 0.898732408 2.64E-184
cg17149495 0.44348659 1.68E-126
cg22802167 0.955548624 0
cg24669183 0.757784612 0
cg17308840 0.289754876 8.45E-182
cg17866181 0.86182894 0
cg24159721 0.107235778 0
cg15174812 0.116825648 0
cg08477687 0.275007441 5.61E-113
cg00034556 0.146131588 0
cg00645010 0.092583111 0
cg15394630 0.119426041 0

Total number of rows: 442308

Table truncated, full table size 11260 Kbytes.




Supplementary file Size Download File type/resource
GSM5732120_3998426090_R02C01_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM5732120_3998426090_R02C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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