|
| Status |
Public on Apr 01, 2012 |
| Title |
4.0N (2009) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumors
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Anal carcinoma
tissue: tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).
|
| Label |
Cy5
|
| Label protocol |
1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).
|
| |
|
| Channel 2 |
| Source name |
Reference pooled 46XX
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Normal female genome
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).
|
| Label |
Cy3
|
| Label protocol |
1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).
|
| |
|
| |
| Hybridization protocol |
All hybridizations were done for 40 hours at 20 rpm and 65C
|
| Scan protocol |
Microarray slides were scanned using an Agilent 2565C DNA scanner and images were analyzed with Agilent Feature Extraction version 10.5 using default settings
|
| Data processing |
The aCGH data from each sorted sample that passed our QC metrics were analyzed in Agilent Genomics Workbench 5.0 using the ADM2 step gram algorithm to identify genomic intervals that were significantly aberrant relative to a normal diploid genome.11 We then ranked the aberrant intervals in each cancer genome based on the relative fold change and the number of annotated genes in each interval.
|
| |
|
| Submission date |
Nov 30, 2011 |
| Last update date |
Apr 01, 2012 |
| Contact name |
Michael Thomas Barrett |
| E-mail(s) |
barrett.michael@mayo.edu
|
| Phone |
480-301-6736
|
| Organization name |
Mayo Clinic Arizona
|
| Department |
Molecular Pharmacology and Experimental Therapeutics
|
| Street address |
13400 East Shea Boulevard
|
| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
| |
|
| Platform ID |
GPL9777 |
| Series (1) |
| GSE34063 |
Clonal Analysis for Identification of Molecular Pathways with Potential Therapeutic Implications in of Rare Gastrointestinal and Endocrine Cancers |
|
