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Sample GSM3736607

Query DataSets for GSM3736607

Status

Public on Apr 04, 2020

Title

Uveal melanoma, sample 70

Sample type

genomic

Source name

primary uveal melanoma, enucleation

Organism

Homo sapiens

Characteristics

cell type: Uveal melanoma
gep: Class 2

Extracted molecule

genomic DNA

Extraction protocol

Genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen) according to standard instuctions.

Label

Cy5 and Cy3

Label protocol

Standard Illumina Protocol

Hybridization protocol

bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K array using standard Illumina protocol

Scan protocol

Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

Description

beta.201404480.01
MM70

Data processing

ChAMP pipeline in R (2.12.4)

Submission date

Apr 26, 2019

Last update date

Apr 05, 2020

Contact name

Matthew G. Field

Organization name

University of Miami

Street address

1501 NW 10th Avenue

City

Miami

State/province

ZIP/Postal code

33136

Country

USA

Platform ID

GPL13534

Series (2)

GSE130354	BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [BeadChip 450K]
GSE130357	BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas

Data table header descriptions
ID_REF
VALUE	Normalized, Batch-Corrected Average Beta (per ChAMP default settings)
Detection Pval

Data table
ID_REF	VALUE	Detection Pval
cg00000957	0.854039091	<0.01
cg00001349	0.783923205	<0.01
cg00001583	0.036958519	<0.01
cg00002028	0.033872101	<0.01
cg00002719	0.022025348	<0.01
cg00002837	0.628976619	<0.01
cg00003202	0.013429603	<0.01
cg00003287	0.631591932	<0.01
cg00004121	0.615925807	<0.01
cg00007036	0.939997585	<0.01
cg00007898	0.018289748	<0.01
cg00008004	0.105162116	<0.01
cg00008647	0.104249142	<0.01
cg00009292	0.115727548	<0.01
cg00009916	0.016203144	<0.01
cg00011717	0.805397971	<0.01
cg00014168	0.679538641	<0.01
cg00015286	0.809614288	<0.01
cg00015930	0.979556618	<0.01
cg00016238	0.937729224	<0.01

Total number of rows: 468484

Table truncated, full table size 13227 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM3736607_9855358028_R03C02_Grn.idat.gz	4.1 Mb	(ftp)(http)	IDAT
GSM3736607_9855358028_R03C02_Red.idat.gz	4.1 Mb	(ftp)(http)	IDAT
Processed data included within Sample table