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RNA-seq of Arabidopsis thaliana spms and wild-type plants inoculated with Pst DC3000 or mock

ABSTRACT: RNA-seq of Arabidopsis thaliana spms and wild-type plants inoculated with Pst DC3000 or mock

PROVIDER: PRJEB63288 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11577579_1.fastq.gz	Fastqsanger.gz
	ERR11577579_2.fastq.gz	Fastqsanger.gz
	ERR11577580_1.fastq.gz	Fastqsanger.gz
	ERR11577580_2.fastq.gz	Fastqsanger.gz
	ERR11577581_1.fastq.gz	Fastqsanger.gz

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Transcriptome analyses of mock- and Pst DC3000-inoculated Arabidopsis thaliana Col-0 plants at normal and elevated temperature

Project description:We performed RNA sequencing of mock-inoculated and Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana (Col-0 accession) plants at normal (23C) and elevated (30C) temperatures. 4-week-old Col-0 plants were pre-incubated at 23C and 30C for 48h and then leaves were syringe-infiltrated with either mock (MgCl2) or DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 30C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were downregulated, upregulated and unchanged at elevated temperature. Temperature-downregulated DC3000-induced genes were enriched for a whole suite of defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

2022-05-05 | GSE152072 | GEO

RNA-seq of Arabidopsis thaliana spms and wild-type plants inoculated with Pst DC3000 or mock

Project description:RNA-seq of Arabidopsis thaliana spermine synthase (spms) mutant and wild-type (Col-0) inoculated with Pseudomonas syringae pv. tomato DC3000 or mock (MgCl2)

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Transcriptome analyses of Pst DC3000-inoculated Arabidopsis thaliana Col-0 and 35S::CBP60g plants at normal and elevated temperature

Project description:We performed RNA sequencing of Pseudomonas syringae pv. tomato (Pst) DC3000-infected A. thaliana Col-0 and 35S::CBP60g plants at normal (23C) and elevated (28C) temperatures. 4-week-old plants were pre-incubated at 23C and 28C for 48h and then leaves were syringe-infiltrated with DC3000 bacterial inoculum. Plants were incubated at their respective temperatures (23C or 28C) for another 24h post-inoculation before tissue collection for RNA extraction. RNA samples for submitted for RNA sequencing and we found different clusters of DC3000-regulated genes that were similarly or differentially regulated between Col-0 and 35S::CBP60g at elevated temperature. Temperature-downregulated DC3000-induced genes in Col-0 plants that were restored in 35S::CBP60g plants were enriched for immunity/defense-related genes, including those essential for host salicylic acid (defense hormone) biosynthesis and accumulation.

2022-05-05 | GSE197771 | GEO

Transcriptome analyses of mock- and Pst DC3000-inoculated Arabidopsis thaliana Col-0 plants at normal and elevated temperature

Project description:Transcriptome analyses of mock- and Pst DC3000-inoculated Arabidopsis thaliana Col-0 plants at normal and elevated temperature

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Transcription profiling of Arabidopsis wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2)

Project description:To reveal the underlying molecular mechanism of GH3.5 action in modulating the SA and auxin pathways, we performed transcriptional profiling of gh3.5-1D plants after infection with or without Pst DC3000(avrRpt2) on a global scale using the Affymetrix Arabidopsis ATH1 GeneChip Experiment Overall Design: Each 3 leaves of plants of 5-week-old wild type Columbia-0 and mutant gh3.5-1D (heterozygous) were inoculated with Pst DC3000(avrRpt2)at 105 cfu mL-1. Leaves were harvested at 0 h (uninoculated) and 48 hours after inoculation. Three biological repeats were performed on Columbia-0 (wild-type, Col-0) and gh3.5-1D (mutant) after infection with or without Pst DC3000(avrRpt2), respectively.

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Transcriptome sequencing of tomato leaves treated with different Pst DC3000 mutant strains

Project description:We designed an experiment to assess ETI and PTI in RG-PtoR using a series of Pst DC3000 strains which have different mutations that allow dissection of the plant immune response. We collected samples at 6 hai and monitored the development of disease in these plants. Plants infiltrated with DC3000 ΔfliC had no disease symptoms due to the recognition of AvrPto and AvrPtoB effectors by Pto. In contrast, when these two effectors were absent, the plants developed speck disease (DC3000 ΔavrPto ΔavrPtoB and DC3000 ΔavrPto ΔavrPtoB ΔfliC strains). Plants infiltrated with the triple mutant showed the greatest disease severity due to the absence of ETI and flagellin-activated PTI induction. This experimental design allowed us to identify gene expression changes associated with flagellin-activated PTI (DC3000 ΔavrPto ΔavrPtoB versus DC3000 ΔavrPto ΔavrPtoB ΔfliC) and Pto/Prf-mediated ETI (DC3000 ΔfliC versus DC3000 ΔavrPto ΔavrPtoB ΔfliC). NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence 'Source Name' was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.

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Project description:As mechanical stimuli, sound vibrations are known to influence various molecular and physiological processes that can ultimately improve crop performance and yield. Microarray analyses were carried out to investigate the global gene expression changes in MicroTom plants subjected to 1000 Hz sound vibration prior to infection with Pst DC300 to test the effectiveness of sound as a priming agent. Data revealed that 1000 Hz pretreatment is effective in eliciting a transcriptional reprogramming in tomato plants grown under normal conditions, but particularly after Pst DC3000 infection. The protective effect of 1000 Hz pretreatment against Pst DC3000 appeared to be mediated by the upregulation of both unique differentially expressed genes (DEGs) involved in cell wall reinforcement, phenylpropanoid pathway and defensive proteins as well as common DEGs associated with boosting plant basal immunity.

2024-04-26 | GSE239448 | GEO

Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2)

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Microarray analysis of med14 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to determine the induction kinetics of transcriptome changes and to identify differentially expressed genes in the Arabidopsis mutant med14 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that med14 exhibited slower kinetcis of transcriptional changes than the wild type after Pst DC3000/avrRpt2 infection, and the induction of a large group of defense genes was suppressed in the med14 mutant. Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 12 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

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Project description:The goal of the microarray experiment was to determine the induction kinetics of transcriptome changes in the Arabidopsis mutant Atelp2, npr1 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that Atelp2 exhibited slower kinetcis of transcriptional changes than the wild type after Pst DC3000/avrRpt2 infection, whereas npr1 did not show significant alteration in the induction kinetics. Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 12 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

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