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Sample GSM2350852 Query DataSets for GSM2350852
Status Public on Nov 01, 2016
Title 10_BA25
Sample type genomic
 
Source name BA25
Organism Homo sapiens
Characteristics tissue: cortex, Brodmann area 25
age: 19
groupid: MDD suicide case
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 9297962043_R01C01
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 0.60246842
cg00000108 0.88007097
cg00000109 0.628108015
cg00000165 0.232384914
cg00000236 0.84730251
cg00000289 0.437622713
cg00000292 0.649351171
cg00000321 0.333697189
cg00000363 0.188592073
cg00000622 0.040702657
cg00000658 0.718405388
cg00000714 0.109472047
cg00000721 0.900129138
cg00000734 0.084326674
cg00000769 0.081590276
cg00000807 0.891344211
cg00000884 0.807856204
cg00000905 0.140360179
cg00000924 0.627844946
cg00000948 0.904917612

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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