|
| Status |
Public on Sep 01, 2013 |
| Title |
Colorectal Normal Tissue-033112-01NB-CytoScanHD |
| Sample type |
genomic |
| |
|
| Source name |
Colorectal Normal Tissue-033112-01NB
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Adjacent Normal
gender: Male
age: 56
tissue: Sigmoid
tnm: T3N0M0
Stage: II
|
| Treatment protocol |
NONE
|
| Growth protocol |
NONE (Tissue samples were used)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA and RNA were extracted from the same tissue using Macherey Nagel trio kit (Germany).10-30mg of tissue sample was homogenized using Qiagen Tissue lyzer. The lysate was loaded on centrifuge columns. After washing nucleic acids were eluted as per the manufacturers protocol.
|
| Label |
Biotin
|
| Label protocol |
CytoScanHD kit and Reagent kit bundle from Affymetrix
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.
|
| Description |
033112-01NB
Hybridized to CytoScanHD
|
| Data processing |
Nexus Copy Number 6.0 (Biodiscovery, Inc., CA, USA) was used to assess genome wide copy number frequencies for the 15 patients. Aroma.affymetrix - another CBS implemented as part of BioConductor’s DNACopy library- and the underlying TumorBoost algorithm were also used to identify genomic events and normalize allele specific copy number with paired normals
Primary data description: CNV calls, LOH (see supplementary file linked on Series record)
|
| |
|
| Submission date |
May 22, 2013 |
| Last update date |
Sep 01, 2013 |
| Contact name |
Sathish Periyasamy |
| E-mail(s) |
sathish.periyasamy@gmail.com
|
| Phone |
0966503921073
|
| Organization name |
NGHA
|
| Department |
Bioinformatics
|
| Street address |
P.O. Box 22490
|
| City |
Riyadh |
| State/province |
Select a State or Province |
| ZIP/Postal code |
11426 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE47204 |
CytoScanHD array Data for Colerectal Tumor and Normal Samples |
|
