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Sample GSM1215449 Query DataSets for GSM1215449
Status Public on Feb 26, 2014
Title Lymph_node_SJ600-5
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 0.580409439
cg00000108 0.958152651
cg00000109 0.897274333
cg00000165 0.233096855
cg00000236 0.878066378
cg00000289 0.689798351
cg00000292 0.770124698
cg00000321 0.404755613
cg00000363 0.408481053
cg00000622 0.007410972
cg00000658 0.818382769
cg00000714 0.277551466
cg00000721 0.902809728
cg00000734 0.084002565
cg00000769 0.038264619
cg00000807 0.740802404
cg00000884 0.897975225
cg00000905 0.061785426
cg00000924 0.545103653
cg00000948 0.877381119

Total number of rows: 485577

Table truncated, full table size 10783 Kbytes.

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

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