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Sample GSM1215414 Query DataSets for GSM1215414
Status Public on Feb 26, 2014
Title Lymph_node_KA522_2
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Lymph_node
gender: male
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from 25 mg samples of the tissue specimens using the NucleoSpin® Tissue kit (Macherey-Nagel GmbH, Düren, Germany)
Label Cy5 and Cy3
Label protocol According to Illumina protocol
Hybridization protocol According to Illumina protocol
Scan protocol According to Illumina protocol
Data processing The raw data were subject to quality control and normalization using the standard protocols suggested for the bioconductor R package minfi. All probes containing single nucleotide polymorphisms and CpG sites from the X and Y chromosomes were removed from the analysis.
matrix processed value definition: Average Beta
matrix signal intensities value definition: Matrix signal intensities (non-normalized) contains unmethylated (signal A) and methylated (Signal B) signal intensities
Submission date Aug 26, 2013
Last update date Feb 26, 2014
Contact name Kaie Lokk
Organization name University of Tartu
Street address Riia 23
City Tartu
ZIP/Postal code 501010
Country Estonia
Platform ID GPL13534
Series (1)
GSE50192 DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns

Data table header descriptions
VALUE minfi normalized signal intensity

Data table
cg00000029 0.356251016
cg00000108 0.921547726
cg00000109 0.766793327
cg00000165 0.168621685
cg00000236 0.853579346
cg00000289 0.584790363
cg00000292 0.709470847
cg00000321 0.410476712
cg00000363 0.253289635
cg00000622 0.002604167
cg00000658 0.8097088
cg00000714 0.140790649
cg00000721 0.95902155
cg00000734 0.07989462
cg00000769 0.052421563
cg00000807 0.766172676
cg00000884 0.910542741
cg00000905 0.10481994
cg00000924 0.566751543
cg00000948 0.859683844

Total number of rows: 485577

Table truncated, full table size 10705 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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