|
Status |
Public on Sep 01, 2013 |
Title |
Colorectal Normal Tissue-031912-01NB-CytoScanHD |
Sample type |
genomic |
|
|
Source name |
Colorectal Normal Tissue-031912-01NB
|
Organism |
Homo sapiens |
Characteristics |
cell type: Adjacent Normal gender: Female age: 56 tissue: Recto-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 |
031912-01NB 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)
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|
|
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 |
|