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Sample GSM5534963

Query DataSets for GSM5534963

Status

Public on Aug 25, 2021

Title

Human Ependymoma Tissue [EPEND350]

Sample type

genomic

Source name

Human Ependymoma Tissue

Organism

Homo sapiens

Characteristics

tissue: Ependymoma
methylation class: PFA
classifier score: 0.99
who grade: III
tumour location: PF
event free survival: 5
overall survival: 5
survival status: D
recurrence: Yes
1q gain: 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

EPEND350

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	0.823184677	0
cg14008030	0.601611774	0
cg12045430	0.148827093	0
cg20826792	0.212264896	0
cg00381604	0.0574527	0
cg20253340	0.480486236	0
cg21870274	0.909471688	0
cg24335620	0.795530431	0
cg16162899	0.929016996	6.84E-303
cg17149495	0.589516678	2.89E-171
cg22802167	0.932404181	0
cg24669183	0.820433482	0
cg17308840	0.731990308	0
cg17866181	0.90450533	0
cg24159721	0.095938428	0
cg15174812	0.126789276	0
cg08477687	0.468618511	7.12E-243
cg00034556	0.153043054	0
cg00645010	0.122082134	0
cg15394630	0.153900365	0

Total number of rows: 438007

Table truncated, full table size 10981 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM5534963_3998426088_R06C01_Grn.idat.gz	4.0 Mb	(ftp)(http)	IDAT
GSM5534963_3998426088_R06C01_Red.idat.gz	4.0 Mb	(ftp)(http)	IDAT
Processed data included within Sample table
Processed data are available on Series record