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| Status |
Public on Jan 01, 2010 |
| Title |
Zebrafish response to microbiota |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
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| Summary |
Vertebrates are colonized at birth by complex microbial communities (microbiota) that influence diverse aspects of host biology. We have used a functional genomics approach to identify zebrafish genes that are differentially expressed in response to the microbiota. We assessed RNA expression profiles from zebrafish larvae at 6 days post-fertilization (dpf) that were either raised continuously in the absence of any microorganism (germ-free or GF), or raised GF through 3dpf then colonized with a normal zebrafish microbiota (conventionalized or CONVD).
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| Overall design |
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. 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 and scanning were performed using standard Affymetrix protocol. Raw expression values were normalized (Invariant set method) and modeled (PM-MM model), and present/absent calls were generated using dChip software (build date Dec.11, 2005).
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| Contributor(s) |
Rawls JF |
| Citation(s) |
21439961 |
| Submission date |
Jun 26, 2009 |
| Last update date |
Jan 25, 2018 |
| 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.
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7545 |
| Country |
USA |
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| Platforms (1) |
| GPL1319 |
[Zebrafish] Affymetrix Zebrafish Genome Array |
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| Samples (6)
|
| GSM422418 |
Germ-free_6dpf_zebrafish_larvae_replicate1_8297 |
| GSM422419 |
Germ-free_6dpf_zebrafish_larvae_replicate2_8298 |
| GSM422420 |
Germ-free_6dpf_zebrafish_larvae_replicate3_8422 |
| GSM422421 |
Conventionalized_6dpf_zebrafish_larvae_replicate1_8299 |
| GSM422422 |
Conventionalized_6dpf_zebrafish_larvae_replicate2_8300 |
| GSM422423 |
Conventionalized_6dpf_zebrafish_larvae_replicate3_8301 |
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| Relations |
| BioProject |
PRJNA117561 |
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