Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana strain:Col-0 or Ler-0

ABSTRACT: High-throughput identification of T-DNA-flanking sequence with sequence capture

PROVIDER: PRJNA287142 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2077950_1.fastq.gz	Fastqsanger.gz
	SRR2077950_2.fastq.gz	Fastqsanger.gz
	SRR2077960_1.fastq.gz	Fastqsanger.gz
	SRR2077960_2.fastq.gz	Fastqsanger.gz
	SRR2077970_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 116

Similar Datasets

Genomic DNA sequences of recombinant F2 individuals from an Arabidopsis thaliana Col X Ler cross

Project description:Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.

2019-08-25 | E-MTAB-8165 | biostudies-arrayexpress

Arabidopsis thaliana strain:Columbia (Col-0)

Project description:Targeted genomic enrichment of long DNA fragments flanking a known core sequence in Arabidopsis thaliana

| PRJNA210809 | ENA

Allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col and Ler reciprocal F1 hybrid embryo and endosperm

Project description:High throughput Illumina sequencing of poly-A selected RNA from Arabidopsis Col and Ler reciprocal F1 hybrid embryo and endosperm tissue isolated at 6-7 days after pollination to identify imprinted genes.

2011-07-18 | GSE30511 | GEO

Mapping QTLs for 15 morpho-metric traits in <i>Arabidopsis thaliana</i> using Col-0 × Don-0 population.

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

Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col-0.

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

Arabidopsis thaliana strain:Col-0

Project description:NADs identification in A. thaliana

| PRJNA312431 | ENA

Arabidopsis thaliana Col-0 pgm1 spsa1 highlight and chilling temperatures proteins LC-MS/MS

Project description:Abiotic stress exposure of plants induces metabolic reprogramming which is tightly regulated by signalling cascades connecting transcriptional with translational and metabolic regulation. Complexity of such interconnected metabolic networks impedes the functional understanding of molecular plant stress response compromising the design of breeding strategies and biotechnological processes. Thus, defining a molecular network to enable the prediction of a plant’s stress mode promises to promote the understanding of stress responsive biochemical regulation and its technological application. Arabidopsis wild type plants and two mutant lines with deficiency in sucrose or starch metabolism were grown under ambient and cold/high light stress conditions. Stress-induced dynamics of the primary metabolome and the proteome were quantified in a mass spectrometry-based high-throughput experiment. Wild type data were used to train a machine learning algorithm to classify mutant lines under control and stress conditions. Multivariate analysis and classification identified a module consisting of 23 proteins enabling the reliable prediction of coupled temperature and light stress conditions. 18 of these 23 proteins displayed putative protein-protein interactions connecting transcriptional regulation with regulation of primary and secondary metabolism under stress. The identified stress-responsive core module provides evidence for predictability of complex biochemical regulation during environmental fluctuation.

2018-11-06 | PXD010580 | Pride

Arabidopsis thaliana strain:Col-0

Project description:Identification of a new gibberellin receptor agonist

| PRJDB15363 | ENA

Arabidopsis thaliana strain:Col-0

Project description:Identification of a new gibberellin receptor agonist

| PRJDB15364 | ENA

Arabidopsis thaliana strain:Col-0

Project description:Identification of a new gibberellin receptor agonist

| PRJDB15360 | ENA