GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1505189 Query DataSets for GSM1505189
Status Public on Sep 17, 2014
Title VAT_76
Sample type genomic
Source name severely obese patient_visceral adipose tissue
Organism Homo sapiens
Characteristics subject status: severely obese patient
gender: female
subject age: 43
bmi: 40.518
tissue: visceral adipose tissue
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified from liver samples using the AllPrep DNA/RNA/Protein Mini kit (QIAgen, Hilden, Germany) according to standard instructions
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting
Description 5822791028_R03C01
Data processing SWAN Normalization and M-value transformation, using minfi (v.1.8.9) and R (v.3.0.2)
Submission date Sep 16, 2014
Last update date Sep 17, 2014
Contact name Lude Franke
Organization name UMCG
Department Genetics
Street address Hanzeplein 1
City Groningen
State/province Please Select
ZIP/Postal code 9713 GZ
Country Netherlands
Platform ID GPL13534
Series (2)
GSE61453 Epigenome analysis of the human visceral adipose tissue
GSE61454 DNA methylation from severely obese samples in liver, muscle, visceral adipose tissue and subcutaneous adipose samples

Data table header descriptions
VALUE SWAN Normalized M-value

Data table
cg00001349 0.762146605
cg00001583 0.093327867
cg00002028 0.053672327
cg00002719 0.073349755
cg00002837 0.390868687
cg00003202 0.025786343
cg00003287 0.247425823
cg00007036 0.93514314
cg00007898 0.035171962
cg00008004 0.076595854
cg00008647 0.106062416
cg00009292 0.168867197
cg00011717 0.922592288
cg00014168 0.702333777
cg00015286 0.829476287
cg00016238 0.867808961
cg00017221 0.105980678
cg00017437 0.078944255
cg00021123 0.638573104
cg00021576 0.039188129

Total number of rows: 399654

Table truncated, full table size 8943 Kbytes.

Supplementary file Size Download File type/resource
GSM1505189_5822791028_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1505189_5822791028_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap