|
| Status |
Public on Feb 01, 2016 |
| Title |
246270_1_Ctx |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: high-grade astrocytoma (HGA) tumor
ID: 246270
genotype: TRPnull
brain location: Ctx
diagnosis: GBM
|
| Treatment protocol |
Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with Qiagen DNeasy kit according to manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
DNA labeling and hybridization were performed in the UNC LCCC Genomics Core using Agilent CGH ULS Protocol v.3.1 according to manufacturer’s instructions.
|
| |
|
| Channel 2 |
| Source name |
Reference DNA pooled from brains of 10 syngeneic littermates
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Reference DNA pooled from brains of 10 syngeneic littermates
|
| Treatment protocol |
Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with Qiagen DNeasy kit according to manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
DNA labeling and hybridization were performed in the UNC LCCC Genomics Core using Agilent CGH ULS Protocol v.3.1 according to manufacturer’s instructions.
|
| |
|
| |
| Hybridization protocol |
DNA labeling and hybridization were performed in the UNC LCCC Genomics Core using Agilent CGH ULS Protocol v.3.1 according to manufacturer’s instructions.
|
| Scan protocol |
Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)
|
| Data processing |
Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD). Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels. Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapsed by averaging.
|
| |
|
| Submission date |
Jul 26, 2013 |
| Last update date |
Feb 01, 2016 |
| Contact name |
Ryan Miller |
| E-mail(s) |
[email protected]
|
| Phone |
919-966-4333
|
| Organization name |
University of North Carolina
|
| Department |
Pathology
|
| Street address |
6109B NRB CB 7250
|
| City |
Chapel HIll |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL15076 |
| Series (2) |
| GSE49268 |
Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 4) |
| GSE49269 |
Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations |
|
