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Sample GSM1215413 Query DataSets for GSM1215413
Status Public on Feb 26, 2014
Title Lymph_node_KA522_1
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 0.37997535
cg00000108 0.899505202
cg00000109 0.798910321
cg00000165 0.184482566
cg00000236 0.807230205
cg00000289 0.666488516
cg00000292 0.667650014
cg00000321 0.390953372
cg00000363 0.228466843
cg00000622 0.012484721
cg00000658 0.825723775
cg00000714 0.16590193
cg00000721 0.929331961
cg00000734 0.075131635
cg00000769 0.059718368
cg00000807 0.767063971
cg00000884 0.895771477
cg00000905 0.072882237
cg00000924 0.530050275
cg00000948 0.888776068

Total number of rows: 485577

Table truncated, full table size 10809 Kbytes.

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

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