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Series GSE16857 Query DataSets for GSE16857
Status Public on Jan 01, 2010
Title Zebrafish response to microbiota
Organism Danio rerio
Experiment type Expression profiling by array
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).
 
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).
 
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.
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7545
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
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
Relations
BioProject PRJNA117561

Download family Format
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Supplementary file Size Download File type/resource
GSE16857_RAW.tar 12.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table
Raw data included within Sample table

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