|
| Status |
Public on Aug 26, 2008 |
| Title |
Expression profile 12 hours post infection for dl1500 virus expressing WT small e1a |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
infected IMR90 fibroblasts total labeled RNA
|
| Organism |
Homo sapiens |
| Characteristics |
infected IMR90 female fibroblasts total labeled RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
qiagen RNAeasy Kit for total RNA extraction. Sample has been extrqacted at 6 hours post infection
|
| Label |
cy5
|
| Label protocol |
Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol G4140-90050 v.5.7
|
| |
|
| Channel 2 |
| Source name |
Mock infected IMR90 fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
Mock infected IMR90 female fibroblasts total labeled RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
qiagen RNAeasy Kit for total RNA extraction. Sample has been extrqacted at 6 hours post infection
|
| Label |
cy3
|
| Label protocol |
Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol G4140-90050 v.5.7
|
| |
|
| |
| Hybridization protocol |
Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol G4140-90050 v.5.7
|
| Scan protocol |
Agilent DNA Microarray Scanner
|
| Description |
none
|
| Data processing |
Triplicate samples of 250 ng of RNA from three independent infections from dl1500- and mock-infected primary IMR90 fibroblasts cells were amplified and labeled with Cy5 and Cy3 (Perkin Elmer), respectively, using the Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Protocol according to manufacturer's instructions. Labeled RNA was hybridized to the Agilent Human whole-genome array (G2534-60011) and Expression data were extracted using Agilent Feature Extraction software (version 9.1.3.1). Raw data was natural log (ln) transformed and signals from multiple probes for the same gene were averaged. Each array was normalized so that the mean was zero and standard deviation was one. Data from three independent replicate experiments were averaged.
|
| |
|
| Submission date |
Jul 08, 2008 |
| Last update date |
Aug 25, 2008 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL7031 |
| Series (2) |
| GSE12045 |
Expression profiles and ChIP on chip genomewide experiments with dl1500 virus (expressing WT small e1a). |
| GSE12543 |
Profiles and ChIP on chip experiments with dl1500 virus (expressing WT small e1a), R2G and deltaCR2 mutant viruses |
|
