|
| Status |
Public on Aug 27, 2009 |
| Title |
colon_INT_T3_snp |
| Sample type |
genomic |
| |
|
| Source name |
Colon, DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age: 70
dimension: 4
stage: IV
status: 1
survival: 4
apc: 1
kras: 1
tp53: 1
chr18qloh: 1
|
| Biomaterial provider |
Fondazione IRCCS Istituto Nazionale dei Tumori (INT)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the QIAamp Tissue Extraction kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix procedures.
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures.
|
| Scan protocol |
Standard Affymetrix procedures using Gene ChIP Scanner 3000.
|
| Description |
Copy number data of sporadic colon cancer patient (INTcartella:9736918, INTistologico:269537I)
|
| Data processing |
Copy number estimates (log-ratios and state) were calculated using Affymetrix v. 1.5.6 CNAT copy-number pipeline. A set of 48 Hapmap samples were used as anun-paired reference set <http://www.affymetrix.com/support/technical/sample_data/500k_data.affx>. All additional analysis was performed in R/Bioconductor and is available as a reproducible Sweave document from <http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html>.
|
| |
|
| Submission date |
May 15, 2009 |
| Last update date |
Aug 19, 2016 |
| Contact name |
James F Reid |
| E-mail(s) |
james.reid@ifom-ieo-campus.it
|
| Organization name |
Fondazione Istituto FIRC di Oncologia Molecolare
|
| Department |
Molecular Genetics of Cancer
|
| Lab |
Cancer genomics
|
| Street address |
Via Adamello, 16
|
| City |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE16125 |
Integrative approach for prioritizing cancer genes in sporadic colon cancer |
|
| Relations |
| Reanalyzed by |
GSE85838 |
