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Sample GSM2350845 Query DataSets for GSM2350845
Status Public on Nov 01, 2016
Title 221_BA11
Sample type genomic
 
Source name BA11
Organism Homo sapiens
Characteristics tissue: cortex, Brodmann area 11
age: 76
groupid: non-psychiatric sudden death
gender: F
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from ~50 mg of each dissected brain region using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.
Label Cy3 and Cy5
Label protocol 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer's standard protocol.
 
Hybridization protocol Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.
Scan protocol Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).
Description 9297962027_R03C02
Data processing Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on Illumina's database and probes identified by Chen et al. (Epigenetics 2013, 8:203-209) were removed. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
 
Submission date Oct 18, 2016
Last update date Nov 01, 2016
Contact name Therese M Murphy
E-mail(s) t.murphy@exeter.ac.uk
Organization name University of Exeter
Department University of Exeter Medical School
Street address RILD building
City Exeter
ZIP/Postal code EX2 5DW
Country United Kingdom
 
Platform ID GPL13534
Series (1)
GSE88890 Major depression MDD suicide brain study

Data table header descriptions
ID_REF
VALUE Normalized Average Beta

Data table
ID_REF VALUE
cg00000029 0.427532482
cg00000108 0.896879112
cg00000109 0.67348937
cg00000165 0.242609057
cg00000236 0.822434329
cg00000289 0.517033464
cg00000292 0.755588614
cg00000321 0.463800991
cg00000363 0.173733149
cg00000622 0.036862417
cg00000658 0.735907596
cg00000714 0.079234355
cg00000721 0.851222437
cg00000734 0.075768706
cg00000769 0.084548576
cg00000807 0.868824927
cg00000884 0.767535606
cg00000905 0.092026996
cg00000924 0.625677074
cg00000948 0.879255777

Total number of rows: 416876

Table truncated, full table size 9321 Kbytes.




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

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