|
| Status |
Public on Mar 01, 2012 |
| Title |
NimbleGen: Human cerebral cortex H1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MeDIP DNA from human cerebral cortex
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age (year): 40
|
| Treatment protocol |
Post-mortem brain samples from cerebral cortex were collected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
Follow standard NimbleGen protocols
|
| |
|
| Channel 2 |
| Source name |
Input DNA from human cerebral cortex
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age (year): 40
|
| Treatment protocol |
Post-mortem brain samples from cerebral cortex were collected
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Follow standard NimbleGen protocols
|
| |
|
| |
| Hybridization protocol |
Follow standard NimbleGen protocols
|
| Scan protocol |
The Scanning was performed with the Axon GenePix 4000B microarray scanner
|
| Description |
Human cerebral cortex DNA methylation
|
| Data processing |
Between array normalization was conducted using Limma package implemented in R, and the probes that were not unique in the respective genomes were removed from the analyses.
|
| |
|
| Submission date |
Feb 23, 2011 |
| Last update date |
Mar 01, 2012 |
| Contact name |
Jinkai Wang |
| Organization name |
University of California, Los Angeles
|
| Street address |
650 Charles E. Young Drive South, CHS 33-228
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-7278 |
| Country |
USA |
| |
|
| Platform ID |
GPL9448 |
| Series (2) |
| GSE27459 |
Human cerebral cortex DNA methylation by MeDIP-Chip |
| GSE27461 |
Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates |
|
