Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia

ABSTRACT: Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Arabidopsis Thaliana

SUBMITTER: Max Planck Institute for Plant Breeding Research

PROVIDER: PRJEB23751 | EVA | 2017-12-06

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	madeira.accessioned.vcf.gz	Vcf
	madeira.vcf.gz	Vcf

Items per page:

1 - 2 of 2

Similar Datasets

Madeiran Arabidopsis thaliana

Project description:Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia

| PRJEB39363 | ENA

Madeiran Arabidopsis thaliana

Project description:Madeiran Arabidopsis Thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia

| PRJEB39074 | ENA

Project description:Madeiran Arabidopsis thaliana reveals ancient long-range colonization and clarifies demography in Eurasia

| PRJEB23751 | ENA

Arabidopsis thaliana

Project description:Genome-wide identification of long range chromatin interactions involved in regulation of gene expression in Arabidopsis thaliana

| PRJNA188501 | ENA

Untargeted primary metabolite profiling in Arabidopsis thaliana

Project description:The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.

2021-12-09 | ST002012 | MetabolomicsWorkbench

Arabidopsis thaliana

Project description:A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range

| PRJNA1033522 | ENA

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

Project description:Background: Analysis of the effect that chromatin structure has on the expression patterns of eukaryotic genes has recently expanded knowledge of the complex influence genome accessibility has on genome function. Interlaced with regular nucleosomal patterning are other mobile and labile sub-nucleosomal-sized protein structures bound to the genome such as transcription factors (TF), initiation complexes, and modified nucleosomes. Results: We present chromatin structure maps of the A. thaliana Col-0 wild-type (in vitro cell culture) combining differential micrococcal nuclease (MNase) digestion and analysis by paired-end next-generation sequencing with RNASeq data to provide insight into the sensitive genomic regions and variable DNA-bound particle size related to transcriptional activity. The landscape of sub-nucleosomal sized particles (subNSPs) has been investigated, revealing the DNA-binding complex positioning genome-wide. We observe the dynamic changes in the distribution of these complexes surrounding genomic features, particularly at transcription start sites (TSS). Differential digestion reveals the presence of MNase-sensitive smaller particles and a labile -1 nucleosome upstream of the TSS of active genes. These changes correlate with gene expression differences resulting from different environmental conditions of light- or dark growth both globally and locally, and a complex profile of bound particles is directly visualised. Conclusions: Analysis of the A. thaliana genome reveals that resolution of chromatin particle size by differential MNase digestion allows detection of the sensitive features in chromatin structure that have hereto been obfuscated. The concomitant analysis of transcript levels reveals the impact of transient extrinsic factors in modifying the sub- nucleosomal landscape in association with transcriptional changes, giving insight into the binding of transcription-associated factors.

2017-08-21 | GSE94377 | GEO

Light acclimation response of the thylakoid proteome in Arabidopsis

Project description:The plant chloroplast thylakoid membrane must respond to environmental variations in light intensity to maximise the efficiency of photosynthesis and minimise photo-oxidative stress. Plants respond to changing light intensity in the short-term (seconds to minutes) through altered regulation of the structure and function of existing thylakoid components, whereas long-term acclimation (hours to days) involves changes in gene expression, protein synthesis and degradation, which modulate the composition of the thylakoid membrane. Here we have investigated the long-term changes in the thylakoid membrane composition in Arabidopsis thaliana plants acclimated to low, moderate and high light intensities using quantitative label-free proteomics in combination with a range of biochemical and spectroscopic functional analyses.

2021-08-23 | PXD014982 | Pride

Small RNAs from Cuscuta campestris parasitizing Arabidopsis thaliana

Project description:Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in high levels of secondary siRNA production. The targeted mRNAs function in hormone perception, pathogen-defense signaling, phloem function, and stem-cell identity. Homologs of these target mRNAs from diverse plants also have high-confidence complementary sites to C. campestris miRNAs, suggesting that homologous mRNAs are targeted by C. campestris across its very broad host range. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

2017-12-18 | GSE84955 | GEO

Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

Project description:Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

| PRJNA665188 | ENA