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Sample GSM1215395 Query DataSets for GSM1215395
Status Public on Feb 26, 2014
Title Lymph_node_BM419/4
Sample type genomic
Source name Autopsy
Organism Homo sapiens
Characteristics tissue: Lymph_node
gender: female
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 0.464306759
cg00000108 0.991536856
cg00000109 0.886764104
cg00000165 0.23415081
cg00000236 0.876759124
cg00000289 0.66550957
cg00000292 0.698420069
cg00000321 0.467761284
cg00000363 0.334899185
cg00000622 0
cg00000658 0.913317952
cg00000714 0.178497636
cg00000721 1
cg00000734 0.095764091
cg00000769 0.040728142
cg00000807 0.795180195
cg00000884 0.975474828
cg00000905 0.082147537
cg00000924 0.585154522
cg00000948 0.906101966

Total number of rows: 485577

Table truncated, full table size 10193 Kbytes.

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

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