NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2350815 Query DataSets for GSM2350815
Status Public on Nov 01, 2016
Title 133_BA11
Sample type genomic
 
Source name BA11
Organism Homo sapiens
Characteristics tissue: cortex, Brodmann area 11
age: 42
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 9297953165_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 0.54578675
cg00000108 0.891467662
cg00000109 0.800443913
cg00000165 0.333608013
cg00000236 0.864215485
cg00000289 0.4902719
cg00000292 0.63661412
cg00000321 0.470098386
cg00000363 0.135972003
cg00000622 0.04607928
cg00000658 0.731419309
cg00000714 0.113024611
cg00000721 0.869665219
cg00000734 0.072959247
cg00000769 0.062610697
cg00000807 0.854898974
cg00000884 0.788379646
cg00000905 0.169440047
cg00000924 0.595601317
cg00000948 0.855692975

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

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