Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1078884 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28037950_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28037951_1.fastq.gz | Fastqsanger.gz | |||
| SRR28037951_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Purpose: The goals of this study are to analyze the transcriptome of Arabidopsis thaliana treated after flg22 and to find changes of glucosinolate metabolism genes after treatment. Methods: Total mRNA of 10 day wild-type Arabidopsis seedlings that were treated with and without flg22( final concentrations 1μmol/L) in 1/2 MS medium for 4h, were extracted respectively. Each sample was harvested in three independent biological replicates with equal weight and mixed ,subsequently sequencing. The sequence reads that passed quality filters were mapped to the Arabidopsis_thaliana genome (TAIR10.18).Then the mapping genes were used for the abundance and functional analysis. Results: We mapped about 45 million and 52 million sequence reads of control sample and treatment sample to the Arabidopsis_thaliana genome (TAIR10.18) and identified total 23,413 genes with Botiw/TopHat workflow. Comparison of the two samples showed 1,200 differentially expressed genes (DEGs), including 290 down-regulated and 910 up-regulated genes. The DEGs were associated with energy metabolism, amino acid metabolism and biosynthesis of secondary metabolites. After flg22 treatment, genes involved in indolic glucosinolate biosynthesis pathway were up-regulated significantly，which is further demonstrated by Real Time RT-PCR, while aliphatic glucosinolate pathway almost had no change, indicating the important role of indolic glucosinolates in plant defense responses. Conclusion: Our study provides the overall genetic resource of Arabidopsis_thaliana after treated by flg22 to date. These data will pave the way for further studies about deeply understand pathogen induced defense and the contribution of indolic glucosinolates.
2017-03-22 | GSE56117 | GEO
Project description:Association Genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. The requirements for many markers and a genome sequence to order those markers have limited its exploitation in crops. To harness this approach for use in a broad range of crops, even those with complex genomes, we developed an approach based on transcriptome sequencing to exploit markers representing variation in both gene sequences and gene expression. We term this approach Associative Transcriptomics. Applying it successfully in Brassica napus, as an example, we identified that genomic deletions including orthologues of the transcription factor controlling aliphatic glucosinolate biosynthesis in Arabidopsis thaliana, HAG1 (At5g61420), underlie two QTL for glucosinolate content of seeds.
2012-07-04 | E-MTAB-4309 | biostudies-arrayexpress
Project description:Helveticoside was a biologically active component of seeds extract of Descurainia Sophia.
| PRJNA273924 | ENA
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Our proteomic and metabolic profile analysis of sweetpotato roots stored at low temperature reveal that the antioxidant enzymes activities, proline and especially soluble sugar content were significantly increased. Most of the DEPs were implicated in phenylpropanoids and followed by starch and sucrose metabolism. Glucosinolate biosynthesis played a leading role in metabolic pathways of sweetpotao roots. More importantly, leucine, tryptophan, tyrosine, isoleucine and valine were all significantly up-regulated in glucosinolate biosynthesis.
2021-09-09 | PXD017728 | Pride
Project description:Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. We used Arabidopsis thaliana mutant lines with disruptions in the indole glucosinolate pathway, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how disrupting this pathway affects the root exudate profile of Arabidopsis thaliana, and in turn, impacts the rhizosphere microbial community. Chemical analysis of the root exudates from the wild type Columbia (Col-0), a mutant plant line overexpressing the MYB transcription factor ATR1 (atr1D) which increases glucosinolate production, and the loss-of-function cyp79B2cyp79B3 double mutant line with low levels of glucosinolates confirmed that alterations to the indole glucosinolate biosynthetic pathway shifts the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. This work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria. Our results suggest that alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.
2023-05-31 | MSV000092068 | MassIVE