|
| Status |
Public on Apr 20, 2015 |
| Title |
PBMC-HIV_infection |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Methylated Genomic DNA from HIV infected twin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood mononuclear cell
infection: HIV+
|
| Treatment protocol |
Immunoprecipitation of methylated DNA was performed using the Methylated-DNA IP Kit (Zymo Research)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from peripheral blood mononuclear cells (PBMCs)using the Qiagen DNeasy kit.
|
| Label |
Cy5
|
| Label protocol |
The NimbleGen Dual-Color DNA labeling Kit was used accordint to the standard operating protocol.
|
| |
|
| Channel 2 |
| Source name |
Methylated Genomic DNA from HIV uninfected twin
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: peripheral blood mononuclear cell
infection: HIV-
|
| Treatment protocol |
Immunoprecipitation of methylated DNA was performed using the Methylated-DNA IP Kit (Zymo Research)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from peripheral blood mononuclear cells (PBMCs)using the Qiagen DNeasy kit.
|
| Label |
Cy3
|
| Label protocol |
The NimbleGen Dual-Color DNA labeling Kit was used accordint to the standard operating protocol.
|
| |
|
| |
| Hybridization protocol |
The NimbleGen Hybridization Kit was used accordint to the standard operating protocol.
|
| Scan protocol |
MS 200 Microarray Scanner and MS 200 Data Collection Software were used according to the standard operating protocol.
|
| Data processing |
DEVA software v.1.2.1 from Nimblegen was used to process the data.
From Log2 ratio data, a 750bp fixed-length window was placed around each consecutive probe followed with Kolmogorov-Smirnov (KS) test, and the resulting score called P-score was the -log10 P-value for each probe. Finally, the methylation peak data was generated from the P score data through merging consecutive probes with the following default conditions: minimum cut-off p-value 2.0, maximum 500 bp spacing and minimum of two probes per peak.
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
Apr 20, 2015 |
| Contact name |
Yinfeng Zhang |
| E-mail(s) |
hkbic.cuhk@gmail.com
|
| Organization name |
The Chinese University of Hong Kong
|
| Street address |
1 shatin road
|
| City |
Hong Kong |
| ZIP/Postal code |
0000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL16284 |
| Series (1) |
| GSE68028 |
The alteration of DNA methylation driven by HIV infection based on a pair of monozygotic twins (MeDIP-chip) |
|
