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Sample GSM2350804 Query DataSets for GSM2350804
Status Public on Nov 01, 2016
Title 230_BA25
Sample type genomic
 
Source name BA25
Organism Homo sapiens
Characteristics tissue: cortex, Brodmann area 25
age: 36
groupid: non-psychiatric sudden death
gender: M
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 9283265107_R06C02
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 0.513904766
cg00000108 0.882158216
cg00000109 0.750011893
cg00000165 0.219099948
cg00000236 0.827057114
cg00000289 0.467148935
cg00000292 0.701047541
cg00000321 0.422352438
cg00000363 0.176769892
cg00000622 0.033440063
cg00000658 0.769687182
cg00000714 0.083773851
cg00000721 0.881425093
cg00000734 0.075739943
cg00000769 0.093963146
cg00000807 0.860346551
cg00000884 0.764549454
cg00000905 0.119327691
cg00000924 0.587203252
cg00000948 0.884434912

Total number of rows: 416876

Table truncated, full table size 9322 Kbytes.




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

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