|
| Status |
Public on Oct 27, 2008 |
| Title |
Control 2 |
| Sample type |
RNA |
| |
|
| Source name |
Control
|
| Organism |
Mus musculus |
| Characteristics |
nonmalignant T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were homogenized for RNA isolation using the TRIZOL reagent (Invitrogen) and purified using Qiagen RNeasy minicolumns.
|
| Label |
biotin
|
| Label protocol |
The RNA is converted into cDNA, then double-stranded cDNA is amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated complementary RNA, the cRNA is purified from the in vitro transcription reaction mixture using the RNeasy system (Qiagen).
|
| |
|
| Hybridization protocol |
Purified cRNA is processed for hybridization on the Mouse Expression-Array-430.2.0 Genechip (Affymetrix, Santa Clara) overnight at 45°C by the Microarray Core Facility of the Dana-Farber Cancer Institute. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
|
| Scan protocol |
Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.
|
| Description |
standard processing performed by Microarray Core of DFCI
|
| Data processing |
Data were loaded onto the DNA-Chip Analyzer (dChip, http://www.dchip.org) program for normalization and quantification. Normalization was performed using the default settings of the dChip software, genes were selected for expression differences higher than 1.5-fold by t test (P< 0.05) or for significant changes (P < 0.05).
|
| |
|
| Submission date |
Sep 26, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Alexei Protopopov |
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
IACS
|
| Street address |
1901 East Rd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE12948 |
Oncogenesis of T-ALL and non-malignant consequences of overexpressing NOTCH1 |
|
| Relations |
| Reanalyzed by |
GSE41385 |
| Reanalyzed by |
GSE119085 |
