Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 9
Release date: Jan 1 2008
Last update date: Jan 25 2018
Access: Public
Dataset link Zebrafish response to Mycobacterium marinum infection (Affymetrix series)

Experimental Protocol


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).

Repositories


GEO

GSE8327

ArrayExpress

E-GEOD-8327

BioProject

PRJNA101317

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Contact


John Rawls
John F. Rawls