|
Status |
Public on Mar 31, 2012 |
Title |
4.9T_025 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Wilms' tumor DNA
|
Organism |
Homo sapiens |
Characteristics |
tissue: Wilms' tumor identifier: 4.9T_025
|
Treatment protocol |
No treatments.
|
Growth protocol |
De-identified archival tumor and normal control tissues were used.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
See publication.
|
Label |
Cy5
|
Label protocol |
The Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis-ULS labeling protocol.
|
|
|
Channel 2 |
Source name |
Normal genomic DNA
|
Organism |
Homo sapiens |
Characteristics |
sample type: control
|
Treatment protocol |
No treatments.
|
Growth protocol |
De-identified archival tumor and normal control tissues were used.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
See publication.
|
Label |
Cy3
|
Label protocol |
The Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis-ULS labeling protocol.
|
|
|
|
Hybridization protocol |
The Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis-ULS hybridization protocol.
|
Scan protocol |
Raw intensity signals for each microarray were captured using an Agilent Microarray Scanner (at 5-micron res), and measured using Agilent Feature Extraction and Analysis software (ver 9.5 ).
|
Description |
Tumor vs. normal genomic DNA.
|
Data processing |
Quantile normalization (MATLAB Bioinformatics Toolbox, R2009a). Probes' chromosomal positions lifted over (LiftOver tool: http://genome.ucsc.edu) to human genome build hg18 (raw data is hg19).
|
|
|
Submission date |
Apr 05, 2011 |
Last update date |
Jun 27, 2018 |
Contact name |
Yidong Chen |
E-mail(s) |
cheny8@uthscsa.edu
|
Phone |
2105629163
|
Organization name |
UT Health Science Center at San Antonio
|
Department |
Population Health Sciences
|
Street address |
8403 Floyd Curl Drive, MSC 7784
|
City |
San Antonio |
State/province |
Texas |
ZIP/Postal code |
78229 |
Country |
USA |
|
|
Platform ID |
GPL13372 |
Series (2) |
GSE28397 |
Copy number alteration in Wilms' tumor with custom-designed miRNA probes |
GSE28401 |
miRNA and Wilms' tumor |
|