|
| Status |
Public on Feb 01, 2016 |
| Title |
245586_BS |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: high-grade astrocytoma (HGA) tumor
ID: 245586
genotype: TRPnull
brain location: BS
batch: 2
subtype: 1
survival (mo): 2.33
diagnosis: A3
|
| Treatment protocol |
Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent. 1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes. Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes. Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.
|
| |
|
| Channel 2 |
| Source name |
Stratagene whole mouse reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Stratagene whole mouse reference RNA
|
| Treatment protocol |
Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent. 1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes. Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes. Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.
|
| |
|
| |
| Hybridization protocol |
Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100) as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.
|
| 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. Samples from different batches were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with no covariates included. Normalized data provided is the filtered, batch combined, non-median centered data used to draw conclusions in the study.
|
| |
|
| 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 |
GPL11202 |
| Series (2) |
| GSE49266 |
Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations (part 2) |
| GSE49269 |
Progression from low- to high-grade astrocytoma is characterized by transcriptomal heterogeneity and genomic number copy alterations |
|
