|
Status |
Public on Aug 17, 2014 |
Title |
superior temporal gyrus_subject_40 |
Sample type |
genomic |
|
|
Source name |
superior temporal gyrus
|
Organism |
Homo sapiens |
Characteristics |
subjectid: 40 barcode: 6042316061_R01C01 ad.disease.status: AD braak.stage: 6 Sex: FEMALE age.blood: 76 age.brain: 80 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.
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|
|
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)
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|
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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 |
GSM1069212 |