|
| Status |
Public on Jan 01, 2010 |
| Title |
Germ-free_6dpf_zebrafish_larvae_replicate2_8298 |
| Sample type |
RNA |
| |
|
| Source name |
Whole 6dpf germ-free zebrafish larvae
|
| Organism |
Danio rerio |
| Characteristics |
strain: C32
age: 6 days post-fertilization (6dpf)
tissue: whole larvae
rearing conditions: gnotobiotic
microbial status: germ-free
replicate: 2 of 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from pooled intact zebrafish larvae (28-80 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 (20ug/replicate) were fragmented using standard methods.
|
| |
|
| 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 germ-free zebrafish larvae
|
| 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 26, 2009 |
| Last update date |
Jun 26, 2009 |
| Contact name |
John F Rawls |
| E-mail(s) |
jfrawls@med.unc.edu
|
| 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) |
| GSE16857 |
Zebrafish response to microbiota |
|
