|
| Status |
Public on Oct 20, 2005 |
| Title |
Adenoviral infected fibroblasts Mu11kB- 0493 |
| Sample type |
RNA |
| |
|
| Source name |
Adenoviral infected quiescent fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
C57/Bl6 MEFs
passage 3
serum starved for 48 hrs.
E1- LacZ Ad infected for 16 hrs.
|
| Treatment protocol |
Primary wildtype mouse embryo fibroblasts were prepared from 13.5 dpc C57Bl/6 embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
biotin-labeled
|
| Label protocol |
We generated biotin-labeled cDNA by in vitro transcription from the RNA.
|
| |
|
| Hybridization protocol |
The cDNA was fragmented before hybridization, and we prepared a hybridization cocktail that included the fragmented cDNA, probe array controls, bovine serum albumin and herring sperm DNA. We hybridized the cDNA to the oligonucleotide probes on the probe array for a 16-h incubation at 45 °C. Immediately after the hybridization, the hybridized probe array underwent an automated washing and staining protocol on an Affymetrix fluidics station.
|
| Scan protocol |
We scanned the DNA chips with the Affymetrix GeneChip scanner and processed the signals by the GeneChip expression analysis algorithm (v.2; Affymetrix).
|
| Description |
Quiescent C57/Bl6 fibroblasts were Ad (E1-E3-LacZ) infected for 16hrs. RNA was then harvested, transcribed to cDNA, and hybridized to a Mu11kB array.
|
| Data processing |
Imported into genespring and normalized per chip by 50th percentile and by gene by median expression
|
| |
|
| Submission date |
Jun 20, 2005 |
| Last update date |
Oct 28, 2005 |
| Contact name |
Zachary Conrad Hartman |
| E-mail(s) |
[email protected]
|
| Phone |
919-684-9197
|
| Organization name |
Duke University
|
| Department |
Surgery
|
| Lab |
Lyerly Lab
|
| Street address |
Research Drive MSRB rm 414
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL76 |
| Series (1) |
| GSE3172 |
Adenovirus infected murine embryonic fibroblasts |
|
| Data table header descriptions |
| ID_REF |
|
| Positive |
Number of probe pairs scored positive |
| Negative |
Number of probe pairs scored negative |
| Pairs |
Number of probe pairs per probe set |
| Pairs Used |
Pairs not masked for some reason |
| Pairs InAvg |
Pairs used in average, excluding those with extremely intense or weak score (quality control measure) |
| Pos Fraction |
Positive Probe pairs/total probe pairs |
| Log Avg |
A measure of hybridization performance (higher is better, 0 = random cross-hybridization) |
| Pos/Neg |
Ratio of positive probe pairs/Negative Probe Pairs |
| VALUE |
Signal Strength�Average difference in intensity between PM and MM cells |
| ABS_CALL |
Present, Absent of Marginal Flag Call�based on probe set decision matrix |
