|
| Status |
Public on Dec 01, 2009 |
| Title |
COG.T.ALL.16 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
T-ALL
|
| Organism |
Homo sapiens |
| Characteristics |
age: 12
gender: Female
treatment regimen: COG 9404
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAGEN DNeasy
|
| Label |
Cy3
|
| Label protocol |
Random primers and the exo-Klenow fragment -based ENZO CGH Labeling Kit (ENZO LIfe Sciences p/n ENZ-42671) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Protopopov A, Feng B, Chin L. Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH). Methods Mol Biol.2008;439:87-100.
|
| |
|
| Channel 2 |
| Source name |
male DNA
|
| Organism |
Homo sapiens |
| Characteristics |
male DNA G147A (Promega, Madison, WI)
|
| Biomaterial provider |
Promega, Madison, WI
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
male DNA G147A (Promega, Madison, WI)
|
| Label |
Cy5
|
| Label protocol |
Random primers and the exo-Klenow fragment -based ENZO CGH Labeling Kit (ENZO LIfe Sciences p/n ENZ-42671) was used to differentially label the test DNA with Cy3-labeled nucleotides and the reference DNA - with Cy5. See for detailes: Protopopov A, Feng B, Chin L. Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH). Methods Mol Biol.2008;439:87-100.
|
| |
|
| |
| Hybridization protocol |
Agilent Oligo aCGH Hybridization Kit (p/n 5188-5220) and Agilent Oligo aCGH Wash Buffers (p/n 5188-5226) were used according to manufacturer protocols.
|
| Scan protocol |
Agilent G2565BA Scanner was used according to manufacturer protocol. Data extraction has been performed with Agilent G2567AA Feature Extraction Software v9.1.
|
| Description |
none
|
| Data processing |
Feature extraction data was obtained using Agilent G2567AA Feature Extraction Software, normalized using LOcally-WEighted regression Scatterplot Smoother
|
| |
|
| Submission date |
Feb 20, 2009 |
| Last update date |
Feb 24, 2009 |
| Contact name |
Alexei Protopopov |
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
IACS
|
| Street address |
1901 East Rd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE14959 |
PTEN and the PI3K/AKT Pathway in T-Cell Acute Lymphoblastic Leukemia |
|
