GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1504972 Query DataSets for GSM1504972
Status Public on Sep 17, 2014
Title Liver_37
Sample type genomic
Source name severely obese patient_liver
Organism Homo sapiens
Characteristics subject status: severely obese patient
subject age: 38
gender: female
bmi: 45.089
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 0.807924099
cg00001583 0.07611638
cg00002028 0.073109799
cg00002719 0.080862938
cg00002837 0.377566383
cg00003202 0.031222556
cg00003287 0.246376696
cg00007036 0.966060101
cg00007898 0.055325928
cg00008004 0.137671901
cg00008647 0.158470134
cg00009292 0.184671212
cg00011717 0.964470168
cg00014168 0.582347714
cg00015286 0.836134138
cg00016238 0.834834717
cg00017221 0.112260091
cg00017437 0.063817797
cg00021123 0.851701451
cg00021576 0.091705853

Total number of rows: 399654

Table truncated, full table size 8943 Kbytes.

Supplementary file Size Download File type/resource
GSM1504972_5822791030_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1504972_5822791030_R04C02_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