|
| Status |
Public on Sep 13, 2014 |
| Title |
frontal cortex_subject_8 |
| Sample type |
genomic |
| |
|
| Source name |
frontal cortex (BA9)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain frontal cortex
diagnosis: schizophrenia
age: 47
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 |
9647450049_R05C01
|
| 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, 2013 (n=34,548) (PMID 233115698) were removed. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions. Unmethylated and methylated signal intensities for each sample can be found on the series record in the file preprocessed_Montreal_data.txt.
|
| |
|
| Submission date |
Sep 12, 2014 |
| Last update date |
Sep 13, 2014 |
| Contact name |
Jonathan Mill |
| Organization name |
University of Exeter
|
| Department |
Medical School, RILD Building
|
| Lab |
Epigenetics
|
| Street address |
RD&E NHS Foundation, Trust Campus, Barrack Rd
|
| City |
Exeter |
| ZIP/Postal code |
EX2 5DW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE61380 |
Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. |
|
