Arabidopsis thaliana strain:Col-0
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10113 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR235273.fastq.gz | Fastqsanger.gz | |||
| DRR235274.fastq.gz | Fastqsanger.gz | |||
| DRR235275.fastq.gz | Fastqsanger.gz | |||
| DRR235276.fastq.gz | Fastqsanger.gz | |||
| DRR235277.fastq.gz | Fastqsanger.gz |
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Project description:Genome wide quantitative trait loci (QTL) mapping was conducted in Arabidopsis thaliana using F2 mapping population (Col-0 × Don-0) and SNPs markers. A total of five linkage groups were obtained with number of SNPs varying from 45 to 59 per linkage group. The composite interval mapping detected a total of 36 QTLs for 15 traits and the number of QTLs ranged from one (root length, root dry biomass, cauline leaf width, number of internodes and internode distance) to seven (for bolting days). The range of phenotypic variance explained (PVE) and logarithm of the odds ratio of these 36 QTLs was found be 0.19-38.17% and 3.0-6.26 respectively. Further, the epistatic interaction detected one main effect QTL and four epistatic QTLs. Five major QTLs viz. Qbd.nbri.4.3, Qfd.nbri.4.2, Qrdm.nbri.5.1, Qncl.nbri.2.2, Qtd.nbri.4.1 with PVE > 15.0% might be useful for fine mapping to identify genes associated with respective traits, and also for development of specialized population through marker assisted selection. The identification of additive and dominant effect QTLs and desirable alleles of each of above mentioned traits would also be important for future research.
| S-EPMC7196571 | biostudies-literature
Project description:Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus the accessibility of these loci for TF binding is highly regulated and determines where and when TF bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana, and define organ-specific regulatory sites and binding motifs of transcription factors at these sites. Results: We coupled the recently described INTACT (Isolation of Nuclei TAgged in specific Cell Types) and ATAC-seq (Assay for Transposase-Accessible Chromatin with highthroughput sequencing) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis, based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions, but are correlated with root-specific expression of distant genes. Importantly these gene-distant sites are enriched for binding motifs of TFs important for root development, as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel genedistant regulatory elements. Conclusion: By coupling the INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity, possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
2018-12-23 | GSE122771 | GEO
Project description:Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus the accessibility of these loci for TF binding is highly regulated and determines where and when TF bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana, and define organ-specific regulatory sites and binding motifs of transcription factors at these sites. Results: We coupled the recently described INTACT (Isolation of Nuclei TAgged in specific Cell Types) and ATAC-seq (Assay for Transposase-Accessible Chromatin with highthroughput sequencing) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis, based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions, but are correlated with root-specific expression of distant genes. Importantly these gene-distant sites are enriched for binding motifs of TFs important for root development, as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel genedistant regulatory elements. Conclusion: By coupling the INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity, possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
2018-12-23 | GSE122770 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62750 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62749 | GEO
Project description:Autopolyploidy is a process whereby the chromosome set is multiplied and it is a common phenomenon in angiosperms. Autopolyploidy is thought to be an important evolutionary force that has led to the formation of new plant species. Despite its relevance, the consequences of autopolyploidy in plant metabolism are poorly understood. This study compares the metabolic profiles of natural diploids and artificial autotetraploids of Arabidopsis thaliana Col-0. Different physiological parameters are compared between diploids and autotetraploids using nuclear magnetic resonance (NMR), elemental analysis (carbon:nitrogen balance) and quantitative real-time PCR (qRT-PCR). The main difference between diploid and autotetraploid A. thaliana Col-0 is observed in the concentration of metabolites related to the tricarboxylic acid cycle (TCA) and ?-amino butyric acid (GABA) shunt, as shown by multivariate statistical analysis of NMR spectra. qRT-PCR shows that genes related to the TCA and GABA shunt are also differentially expressed between diploids and autotetraploids following similar trends as their corresponding metabolites. Solid evidence is presented to demonstrate that autopolyploidy influences core plant metabolic processes.
| S-EPMC4876396 | biostudies-literature
Project description:Cell-based reporting system of primary TF targets.
| PRJNA234383 | ENA
Project description:We evaluated differential RNA-seq coverage of all TAIR10-annotated introns in Arabidopsis seedlings subjected to heat stress. Transcriptome analyses of plants infected with bacteria suggested the untreated upf1-5 mutant was enriched not only with pathogen defense-associated mRNAs but also with transcripts encoding genes involved in the general abiotic stress responses. Therefore, we reasoned that global IR events in the upf1-5 mutant and in environmentally stressed wild-type plants may show similarities. Indeed, the transcriptomes of upf1-5 mutant and the heat-stressed wild-type seedlings shared an overlapping set of differentially expressed introns
2014-12-05 | E-MTAB-4292 | biostudies-arrayexpress
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Project description:The gene-body chromatin modifications dynamics mediates epigenome differentiation in Arabidopsis
| PRJDB5192 | ENA