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E-GEOD-8319

ABSTRACT: Transcription profiling by array of Arabidopsis mutant for rlk1 after treatment with chitooctaose

OTHER RELATED OMICS DATASETS IN: PRJNA101301

PROVIDER: E-GEOD-8319 | ExpressionAtlas | 2014-07-08

REPOSITORIES: ExpressionAtlas

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Dataset's files

Source:

			Action	DRS
	E-GEOD-8319-analysis-methods.tsv	Tabular
	E-GEOD-8319-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-8319-configuration.xml	Xml
	E-GEOD-8319-configuration.xml.beforeQC	Xml
	E-GEOD-8319-percentile-ranks.tsv	Tabular

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RNAseq analysis of the transcriptome of an Arabidopsis mutant, ahl13, elicitated by pstDC3000 or flg22

Project description:Purpose: The experiment is to compare the NGS-derived seedling and leaf transcriptome profiling (RNAseq) of an Arabidopsis mutant ahl13 with that of wild type upon bacterial pathogen (pst DC3000) and flagellin elicitation. Method： The mRNA profiles of 10-day-old wild-type (WT) and AHL13 knockout (ahl13, SALK_014014) Arabidopsis were generated by RNAseq using Illumina NovaSeq6000. The sequence reads were passed through quality filters and mapped to Arabidopsis genome by TopHat2 followed by transcript splicing and quantitation by Cufflinks. DESeq was done to analyze differential gene expressions. qRT–PCR validation was performed using SYBR Green assays Result: We mapped about 20 million sequencing reads per sample to the Arabidopsis genome and identified approximately 28,000 transcripts in the Arabidopsis Col-0 and ahl13 mutant using TopHat2. Differentially expressed genes were identified using DESeq2 and about 166 genes show up-regulation in ahl13 upon DC3000 infection (FC>2, FDR<0.01) Conclusions: The ahl13 mutant exhibit differential transcription profile from that of Col-0 upon DC3000 treatment but similar upon flg22 treatment.

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