NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1443524 Query DataSets for GSM1443524
Status Public on Aug 17, 2014
Title entorhinal cortex_subject_61
Sample type genomic
 
Source name entorhinal cortex
Organism Homo sapiens
Characteristics subjectid: 61
barcode: 6969568082_R04C01
ad.disease.status: C
braak.stage: 2
Sex: FEMALE
age.blood: NA
age.brain: 90
source tissue: entorhinal cortex
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from ~100 mg of each dissected brain region or whole blood stored in EDTA collection tubes using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.
Label Cy5 and Cy3
Label protocol 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.
 
Hybridization protocol Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).
Scan protocol Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina HiScan System (Illumina).
Description [[]]
Data processing Illumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization). Data was then pre-processed in the R package wateRmelon using the dasen function. Array data for each of the tissues was normalized separately.
processed data: dasen normalized beta (betas.csv)
raw data: Unmethylated and methylated signal intensities (signal_intensities.csv)
 
Submission date Jul 23, 2014
Last update date Aug 17, 2014
Contact name Leonard C Schalkwyk
E-mail(s) Leonard.Schalkwyk@kcl.ac.uk
Organization name King's College London
Department IOP-SGDP
Street address De Crespigny Park
City London
ZIP/Postal code SE5 8AF
Country United Kingdom
 
Platform ID GPL13534
Series (1)
GSE59685 Cross-tissue methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer’s disease neuropathology
Relations
Reanalysis of GSM1069039

Supplementary data files not provided
Processed data are available on Series record

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