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Series GSE8327 Query DataSets for GSE8327
Status Public on Jan 01, 2008
Title Zebrafish response to Mycobacterium marinum infection (Affymetrix series)
Organism Danio rerio
Experiment type Expression profiling by array
Summary Mycobacteria infect macrophages that aggregate with additional macrophages and lymphocytes to form granulomas. We have used a functional genomics approach to identify immune response genes expressed during granuloma formation in Mycobacterium marinum-infected transparent zebrafish larvae where individual infection steps can be viewed in real time. We assessed RNA expression profiles from zebrafish larvae that were either infected with Mycobacterium marinum, mock-infected, or uninfected. Zebrafish infections were performed at 1 day post-fertilization (dpf), and samples were derived from pools of 6dpf zebrafish larvae.
Keywords: host response to infection
Overall design 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. 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. 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) Pozos TC, Volkman HE, Rawls JF, Ramakrishnan L
Citation(s) 20007864
Submission date Jun 28, 2007
Last update date Jan 25, 2018
Contact name John F Rawls
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 (9)
GSM206399 Wild-type_Mm-infected_rep1_10747
GSM206400 Wild-type_Mm-infected_rep2_10748
GSM206401 Wild-type_Mm-infected_rep3_10749
BioProject PRJNA101317

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Supplementary file Size Download File type/resource
GSE8327_RAW.tar 16.0 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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