|
Status |
Public on Jan 01, 2010 |
Title |
Germ-free_6dpf_zebrafish_larvae_replicate3_8422 |
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: 3 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 |
|