NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2350803 Query DataSets for GSM2350803
Status Public on Nov 01, 2016
Title 183_BA25
Sample type genomic
 
Source name BA25
Organism Homo sapiens
Characteristics tissue: cortex, Brodmann area 25
age: 64
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 9283265107_R06C01
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 0.485248608
cg00000108 0.908001253
cg00000109 0.71329364
cg00000165 0.212596261
cg00000236 0.794890402
cg00000289 0.559395312
cg00000292 0.679695674
cg00000321 0.34107941
cg00000363 0.1488701
cg00000622 0.03207591
cg00000658 0.814579099
cg00000714 0.075379988
cg00000721 0.878842514
cg00000734 0.079047878
cg00000769 0.095987256
cg00000807 0.876232745
cg00000884 0.793311525
cg00000905 0.104662365
cg00000924 0.579379794
cg00000948 0.902584177

Total number of rows: 416876

Table truncated, full table size 9322 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap