|
Status |
Public on Aug 27, 2009 |
Title |
colon_INT_T31_snp |
Sample type |
genomic |
|
|
Source name |
Colon, DNA
|
Organism |
Homo sapiens |
Characteristics |
gender: F age: 83 dimension: 3 stage: II status: 0 survival: 102 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:9805494, INTistologico:272259I)
|
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 |