|
| Status |
Public on Aug 17, 2014 |
| Title |
superior temporal gyrus_subject_80 |
| Sample type |
genomic |
| |
|
| Source name |
superior temporal gyrus
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: 80
barcode: 6042316053_R03C02
ad.disease.status: AD
braak.stage: 4
Sex: FEMALE
age.blood: 79
age.brain: 84
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 |
GSM1069205 |
