Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Sep 23 2016
Last update date: Nov 29 2017
Access: Public
Taxon: Arabidopsis thaliana
Dataset link Expression data from elicitor-treated Arabidopsis seedling roots [3h]

Experimental Protocol


RNA was extracted from roots of seedlings treated with cellobiose, chito-oligomers, OGs or a no-elicitor control, for 3 hours using Trizol LS (Invitrogen) according to the manufacturer's recommendations. RNA integrity was checked with an Agilent 2100 BioAnalyzer. An aliquot from each RNA sample was used as a template to make cDNA, which was assessed by qRT-PCR to confirm that samples had the expected WRKY30 expression profile at 3 hours post-treatment. Samples were then analyzed for gene expression with Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays, using standard Affymetrix reagents and protocols at the QB3-Functional Genomics Lab at the University of California, Berkeley. Samples from three biological replicas for each treatment were analyzed. A total of 24 chips were used (4 treatments x 2 time points x 3 biological replicates). Microarray data were analyzed using the GCRMA algorithm as described previously (Fletcher et al., 2011); ratios of normalized probe set intensity values were calculated for each sample pair (in which M value = log2 [elicitor/control]) and then averaged among the three replicates.

Repositories


GEO

GSE87216

BioProject

PRJNA343981

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Contact


Clarice de Azevedo Souza