GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1504956 Query DataSets for GSM1504956
Status Public on Sep 17, 2014
Title Liver_114
Sample type genomic
Source name severely obese patient_liver
Organism Homo sapiens
Characteristics subject status: severely obese patient
subject age: 49
gender: female
bmi: 36.332
tissue: liver
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 Liver sample of Morbidly patient
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)
GSE61446 Epigenome analysis of the human liver
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 0.776031232
cg00001583 0.075852475
cg00002028 0.05249656
cg00002719 0.31628403
cg00002837 0.479088759
cg00003202 0.03510387
cg00003287 0.202125745
cg00007036 0.949416359
cg00007898 0.056500301
cg00008004 0.136714219
cg00008647 0.094916366
cg00009292 0.148643693
cg00011717 0.924479564
cg00014168 0.517873402
cg00015286 0.758020171
cg00016238 0.803922909
cg00017221 0.091174565
cg00017437 0.121258989
cg00021123 0.858007574
cg00021576 0.103980308

Total number of rows: 399654

Table truncated, full table size 8943 Kbytes.

Supplementary file Size Download File type/resource
GSM1504956_5822791018_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1504956_5822791018_R05C02_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