|
| Status |
Public on Jun 30, 2020 |
| Title |
STG_subject01488_NPC_rep1 [X1488.C] |
| Sample type |
genomic |
| |
|
| Source name |
postmortem STG of NPC subject 1488
|
| Organism |
Homo sapiens |
| Characteristics |
group2: Control
Sex: Male
race: Black
age (years): 39
postmortem interval (hours): 21.5
mechanism of death: Natural
illness duration (years): 0.0
tissue: postmortem superior temporal gyrus (STG)
molecule subtype: bisulfite-treated genomic DNA
|
| Treatment protocol |
Bisulfite conversion of 10 micrograms genomic DNA was performed with the EZ DNA methylation kit (Zymo Research).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA (~10 micrograms) was isolated from STG grey matter (~20 micrograms) using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Valencia, CA, USA).
|
| Label |
Cy3/Cy5
|
| Label protocol |
Following manufacturer's protocol
|
| |
|
| Hybridization protocol |
Following manufacturer's protocol
|
| Scan protocol |
Following manufacturer's protocol
|
| Data processing |
Data analyses of raw image array files were performed using the R software environment (www.r-project.org). Color adjustment and background correction were performed using the bgAdjust2C method. Before filtering, normalization was performed using the preprocessQuantile method. In data quality control analysis, probe data for each sample demonstrated mean detection p-values<0.05, so no data was exluded due to failed detection for any sample. At the filtering stage, data from any probes that failed detection in any sample at p>=0.01 (N=12,350) were removed from the dataset. Data from probes on sex chromosomes (N=18,628) and from probes with known SNPs (N=27,395) in any sample were removed from the dataset. Probes that cross-react with multiple genomic regions (N=39,269) were also removed. The remaining data presented here reflects signals at 768,268 probes.
The 'processed_data.txt' contains the normalized (preprocessQuantile method) and Averaged Beta (for 8 subject samples replicated) values.
|
| |
|
| Submission date |
Feb 06, 2020 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Brandon Chad McKinney |
| E-mail(s) |
mckinneybc@upmc.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Psychiatry
|
| Street address |
3811 O'Hara Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE144910 |
DNA methylation in the superior temporal gyrus of 44 subjects with schizophrenia and 44 non-psychiatric control subjects |
|
