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Sample GSM1443545 Query DataSets for GSM1443545
Status Public on Aug 17, 2014
Title superior temporal gyrus_subject_67
Sample type genomic
 
Source name superior temporal gyrus
Organism Homo sapiens
Characteristics subjectid: 67
barcode: 6042316063_R03C01
ad.disease.status: AD
braak.stage: 4
Sex: MALE
age.blood: 80
age.brain: 82
source tissue: superior temporal gyrus
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 GSM1069146

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

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