|
| Status |
Public on Feb 16, 2012 |
| Title |
6 hrs post-TPA |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Infected A20 B cells
|
| Organism |
Mus musculus |
| Characteristics |
infection: recombinant murid herpesvirus 4 (MHV68 BAC derived virus harboring hygromycin-enhanced green fluorescent protein)
timepoint: 6 hrs
|
| Treatment protocol |
For experimental Cy3 samples: A20 HE2 cells were treated with 20 nanograms per ml of 12-O-Tetradecanoylphorbol-13-acetate. For reference Cy5-labeled RNA: Cells were infected in MHV68 WUMS strain at multiplicity of infection of 10 plaque forming units per ml.
|
| Growth protocol |
For experimental Cy3 samples: A20 HE2 cells were maintained in RPMI supplemented with 10% serum and 300 microgram per ml hygromycin. For reference Cy5-labeled RNA: NIH 3T3 fibroblasts were cultured in DMEM supplemented in 10% serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Qiagen midi RNA kit following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
2.5 µg of total RNA were labeled using Aglient “Quick Amp Labeling Kit Two-color” following manufacturer's instructions. Spike-in controls were labeled using Agilent “Two-color Spike-in Kit" following manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Infected NIH 3T3 fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
infection: murid herpesvirus 4 (MHV68 WUMS strain)
timepoint: 8 hrs reference
|
| Treatment protocol |
For experimental Cy3 samples: A20 HE2 cells were treated with 20 nanograms per ml of 12-O-Tetradecanoylphorbol-13-acetate. For reference Cy5-labeled RNA: Cells were infected in MHV68 WUMS strain at multiplicity of infection of 10 plaque forming units per ml.
|
| Growth protocol |
For experimental Cy3 samples: A20 HE2 cells were maintained in RPMI supplemented with 10% serum and 300 microgram per ml hygromycin. For reference Cy5-labeled RNA: NIH 3T3 fibroblasts were cultured in DMEM supplemented in 10% serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Qiagen midi RNA kit following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
2.5 µg of total RNA were labeled using Aglient “Quick Amp Labeling Kit Two-color” following manufacturer's instructions. Spike-in controls were labeled using Agilent “Two-color Spike-in Kit" following manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
825 ng linearly amplified cRNA and hybridization buffer were added, and samples were applied to microarrays at 65 degrees C for 17 hrs.
|
| Scan protocol |
Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).
|
| Description |
Custom tiled microarray
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and Agilent default normalization. Spike-in controls were used to calculate scale factor.
|
| |
|
| Submission date |
Feb 16, 2012 |
| Last update date |
Feb 16, 2012 |
| Contact name |
Laurie Krug |
| Organization name |
Stony Brook University
|
| Department |
Molecular Genetics and Microbiology
|
| Street address |
130 Life Sciences Bldg
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL15245 |
| Series (2) |
| GSE35865 |
Tiled Array Experiment of Murine Gammaherpesvirus 68 Transcripts Upon TPA-Stimulated Reactivation From Latency |
| GSE35866 |
Tiled Microarray Identification of Novel Viral Transcript Structures and Distinct Transcriptional Profiles During Two Modes of Productive Murine Gammaherpesvirus 68 Infection. |
|
