Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq of camta3/dsc1/dsc2 after elf18 or mock treatment, against wt control, at 10, 30 and 90 minutes

ABSTRACT: The general stress response is a major transcriptional reprogramming in elicitor response. CAMTA3 is a key regulator of the general stress response, and is guarded by Dominant Suppressor of CAMTA3 1 and DSC2. Here we assay transcriptional response to elf18, an elicitor, at 10 (primary response), 30 (major GSR) and 90 (beginning to be immunity-specific responses) minutes, in wt and in a line mutated in camta3/dsc1/dsc2, thus losing the GSR with only partial autoimmune activation.

INSTRUMENT(S): BGISEQ-500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Cyril Zipfel

PROVIDER: E-MTAB-10210 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of wt and receptor mutant lines in response to 7 elicitor treatments over a 6-point time course

Project description:The degree to which plants discriminate among elicitors in early transcriptional responses is unknown. To test this, we selected a panel of seven elicitors recognized by the model plant Arabidopsis thaliana. Two-week old Arabidopsis seedlings in liquid culture were treated with each elicitor individually, and tissue flash-frozen at 0, 5, 10, 30, 90, and 180 min post-treatment. As a control, receptor mutants for each elicitor were treated and harvested in parallel with wt plants. The experiment was repeated four times. mRNA was extracted via pulldown of poly-A tail from bulk lysate, and libraries were prepared via tagmentation with custom Tn-5 adapter oligos. Libraries for each experiment were pooled, and sequenced across 2-3 flowcells of a NextSeq500 benchtop sequencer.

2021-01-29 | E-MTAB-9694 | biostudies-arrayexpress

RNAseq of Arabidopsis seedlings of either wt or hsl3-1, in response to a 30 minute treatment of 100 nM CTNIP4 relative to mock

Project description:In order to identify novel stress-induced signalling peptides, we searched for Arabidopsis thaliana transcripts encoding short proteins (<150 amino acids) with a predicted signal peptide, which were induced upon biotic elicitor treatment (Bjornson et al., 2021). Through this analysis, we identified an uncharacterised family of peptides with 5 predicted members, which we named CTNIP1 to 5 (pronounced catnip) based on relatively conserved residues within the peptides. CTNIP4 is perceived by Arabidopsis, inducing some hallmark outputs of defence (Pattern-Triggered Immunity) signalling. Mass spectrometric analyses indicated that HSL3 may be the receptor mediating CTNIP recognition. Through assaying transcriptomic responses in wild type and hsl3-1 mutants, we were able to confirm similarity of CTNIP and defence responses at the transcriptional level, and the dependence of these responses on HSL3.

2022-06-13 | E-MTAB-11093 | biostudies-arrayexpress

Transcription profiling of elicitor treatment over time (0, 30, 60 min) in Arabidopsis Landsberg (wt) and fls2-17 (flagellin receptor mutant)

Project description:Transcriptional changes upon elicitor treatment over time (0, 30, 60 min) have been analysed with the A.thaliana Landsberg (wt) and fls2-17 (flagellin receptor mutant).

2006-03-15 | E-MEXP-547 | biostudies-arrayexpress

RNAseq of wild type Col-0 Arabidopsis plants and piezo/feronia/camta3 mutants before and 22 minutes after touch treatment

Project description:RNAseq of wild type Col-0 Arabidopsis plants and piezo/feronia/camta3 mutants before and 22 minutes after touch treatment with a gentle paint brush. The mutants were defective in genes involved in mechanosensing and downstream signalling. Their contribution to touch-responsive signalling was assessed by transcriptome analysis.

2022-08-21 | E-MTAB-10920 | biostudies-arrayexpress

Transcription profiling of Arabidopsis seedlings treated with chitosan

Project description:We treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis (GeneChip microarrays) in order to identify genes and transcription factors regulated by chitosan. The results showed that jasmonate and defense responsive genes, camalexin and lignin biosynthetic genes were among genes up-regulated by chitosan. Several transcription factors are also strongly induced by chitosan. The results suggested that chitosan can be used as a strong elicitor of defense pathways. Experiment Overall Design: Arabidopsis thaliana, ecotype Columbia (Col-0) seeds were sterilized for 7 min in 1.7% (v/v) bleach solution, incubated over night in 4% PPM (Plant Preservative Mixture, Plant Cell Technology, Washington DC, USA) in a full strength sterilized Murashige-Skoog (MS) salt solution with gentle shaking. Subsequently, the seeds were rinsed in abundant sterile water and transferred into 2.5 ml liquid growing media (MS half strength solution) with 0.05% PPM in 6-well plates. The plates were incubated in the dark at 4 Â°C for two days and finally transferred to continuous light (90Âµm photons/ m-2) with gentle swirling for four days in a plant growth chamber at 22 Â°C. Experiment Overall Design: . Treatments were performed by comparing a control solution containing the solvent used to solubilize chitosan, and a chitosan solution concentrated 150 Âµg/ml.

2009-11-10 | E-GEOD-17193 | biostudies-arrayexpress

Transcription profiling of Arabidopsis thaliana wild type Col-0) and Atpdr2 mutant roots.

Project description:To determine the pleiotropic effect of the ABC transporter gene (Atpdr2) mutation, we performed the microarray analyses on the root tissues of Arabidopsis thaliana wild type (Col-0) and Atpdr2 mutant.

2009-10-20 | E-TABM-821 | biostudies-arrayexpress

RNA-seq of 10-day-old Arabidopsis seedlings of Col-0, cpl3 mutant, and pentuple-della mutant genotype

Project description:C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3 (CPL3) is a phosphatase that interacts with the DELLA proteins RGA and GAI, promoting their function. We examined whether CPL3 is involved in regulating the activity of DELLAs, in particular regarding their function in controlling gene expression. For this purpose, we profiled the transcriptome of the cpl3-3 mutant and compared it with that of the dellap (pentuple della) mutant in the same conditions. 10-day-old plants were used to extract RNA with the miRNeasy Mini Kit (Qiagen). The RNAs were first selected via enrichment of their poly(A) tail and then further fragmented into 300~350 bp fragments to build the libraries. Then, the libraries were sequenced on BGIseq500 platform (BGI, Shenzhen, China), the raw data of FASTQ format were firstly processed through in-house Perl scripts. Next, clean reads were aligned to the Arabidopsis reference genome (TAIR10) using HISAT2. StringTie2 was used to count the reads numbers mapped to each gene and the R package DESeq2was used for differential expression analysis. The principal component analysis (PCA) and Pearson correlation were analyzed by the in-house R Script. All experiments were performed in three biological replicates.

2024-04-18 | E-MTAB-13956 | biostudies-arrayexpress

RNA-seq of Arabidopsis thaliana Col-0 seedlings treated with a Cutin Oligomeric Mixture (COM) able to elicit Pattern Triggered Immunity (PTI)

Project description:Seedlings of Arabidopsis thaliana Col-0 were treated with a cutin oligomeric mixture (COM) for 30 min. To evaluate if such treatment was able to induce transcriptional reprogramming related with plant immunity. The transcriptomic profiles were compared with those of the Mock treatment. The list of differentially expressed genes was generated to evaluate similarities with the profiles obtained with treatments with well described plant immune elicitors.

2023-10-31 | E-MTAB-12956 | biostudies-arrayexpress

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

Project description:DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase Pol IV transcribes target sequences to initiate 24-nt siRNA production and action. The Arabidopsis DTF1/SHH1 has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. Taken together, our results show that DTF1 is a core component of the RdDM pathway. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci. Examination of whole-genome DNA methylation and small RNA in 12-day-old Col-0, dtf1-2, nrpd1-3 and nrpe1-11 seedlings

2013-06-03 | E-GEOD-44209 | biostudies-arrayexpress

Transcription profiling by array of genes regulated by ahk2 ahk3 in response to cold in Arabidopsis thaliana

Project description:The experiment was designed to enable comparison of ahk2 ahk3 double mutant in response to cold compared with wild types.

2013-08-14 | E-MEXP-3714 | biostudies-arrayexpress