|
| Status |
Public on Jan 24, 2013 |
| Title |
CCNY17_SNP |
| Sample type |
genomic |
| |
|
| Source name |
Human intrahepatic cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: intrahepatic cholangiocarcinoma (ICC)
icc subclass: Proliferation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Using formalin-fixed, paraffin-embedded HCC tissues, genomic DNA was extracted using QIAcube and QIAGEN spin columns (QIagen).
|
| Label |
Cy5
|
| Label protocol |
Refer to the Illumina CytoSNP12 System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina CytoSNP12 System Manual
|
| Scan protocol |
Refer to the Illumina CytoSNP12 System Manual
|
| Data processing |
Raw data were normalized based on reference cluster file provided by Illumina using GenomeStudio software. Segmented DNA copy number was estimated by using CBS algorithm ("poor-functioning" probes designated by Illumina were removed). NaN indicates locus called as gap by the CBS algorithm.
|
| |
|
| Submission date |
Oct 29, 2011 |
| Last update date |
Jan 24, 2013 |
| Contact name |
Yujin Hoshida |
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL8856 |
| Series (2) |
| GSE33326 |
DNA copy number profiles of formalin-fixed, paraffin-embedded human intrahepatic cholangiocarcinoma |
| GSE33327 |
Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes |
|
