|
| Status |
Public on Mar 31, 2012 |
| Title |
3.8T_012 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Wilms' tumor DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Wilms' tumor
identifier: 3.8T_012
|
| 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 |
|
