|
| Status |
Public on Aug 29, 2011 |
| Title |
Wilms' Tumor T1 |
| Sample type |
genomic |
| |
|
| Source name |
Total DNA from Wilms' Tumor T1
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Wilms' Tumor
agedx: 8
gender: FEMALE
central pathology (rcpat): FAVOR
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments and fractionated on a 1% agarose gel. The extracted fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.
|
| Label |
cy3
|
| Label protocol |
2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
|
| |
|
| Hybridization protocol |
The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/methylation_userguide_v5p0.pdf).
|
| Scan protocol |
Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol.
|
| Description |
50369
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan v2.5 software.
|
| |
|
| Submission date |
May 18, 2011 |
| Last update date |
Aug 29, 2011 |
| Contact name |
Yun Liu |
| E-mail(s) |
yliu39@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Street address |
130 Dong An Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL13611 |
| Series (1) |
| GSE29374 |
DNA copy number variation from human Wilms' Tumor samples |
|
