|
| Status |
Public on Jan 01, 2008 |
| Title |
Wild-type_Mm-infected_rep1_10747 |
| Sample type |
RNA |
| |
|
| Source name |
Whole 6dpf zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf
|
| Organism |
Danio rerio |
| Characteristics |
Strain: AB, Age: 6 days post-fertilization (6dpf), Tissue: whole larvae, Rearing conditions: conventional, Microbial status: infected with Mycobacterium marinum wild-type strain, Days post-infection: 5, Replicate: 1 of 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from pooled intact zebrafish larvae (31-82 larvae/pool, 3 biological replicate pools/condition) using Trizol reagent (Invitrogen) followed by DNase I digestion (DNA-Free, Ambion) according to manufacturers' protocols.
|
| Label |
biotin
|
| Label protocol |
Total RNA from each replicate pool (12ug RNA/replicate) was used as template for independent cDNA synthesis and in vitro transcription reactions (BioArray HighYield RNA Transcript Labeling Kit; Enzo Life Sciences) to generate biotinylated cRNA targets. cRNA targets (30ug/replicate) were fragmented using standard methods. For detailed protocols, see http://pathimm.wustl.edu/~mgacore/protocols.htm
|
| |
|
| Hybridization protocol |
Hybridization performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
|
| Scan protocol |
Scanning performed using standard Affymetrix protocol available at http://www.affymetrix.com/support/technical/manuals.affx
|
| Description |
Whole 6dpf zebrafish larvae infected with Mycobacterium marinum wild-type strain at 1dpf
|
| Data processing |
Raw expression values were normalized (Invariant set method) and modelled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).
|
| |
|
| Submission date |
Jun 28, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
John F Rawls |
| E-mail(s) |
[email protected]
|
| Phone |
919-966-8340
|
| Fax |
919 966-6927
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Department of Cell and Molecular Physiology
|
| Street address |
111 Mason Farm Rd.
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7545 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE8327 |
Zebrafish response to Mycobacterium marinum infection (Affymetrix series) |
|
