Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of NLP7 direct targets using ChIP-chip in Arabidopsis thaliana

ABSTRACT: Chromatin immunoprecipitation was performed in nlp7-1 Arabidopsis thaliana seedlings complemented by a pNLP7::NLP7-GFP construct upon 10 minutes NO3- resupply after a 3-day NO3- starvation. Genome-wide profiling of NLP7 binding regions by ChIP-chip, 2 biological replicates in dye-swap

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: FranM-CM-'ois ROUDIER

PROVIDER: E-GEOD-36763 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Methylome analysis of Arabidopsis thaliana Col-0 primary root

Project description:DNA methylation profiling in Col-0 wild type primary root 2 biological replicates in dye-swap - MeDIP-chip

2012-12-07 | E-GEOD-36750 | biostudies-arrayexpress

Transcriptome analysis of nerd1-1 mutant seedlings

Project description:Expression profiling in nerd1-1 mutant seedlings 2 biological replicates in dye-swap - RNA-chip

2012-12-20 | E-GEOD-35345 | biostudies-arrayexpress

Transcriptome and methylome analyses of the nerd1-1 mutant

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-12-20 | E-GEOD-35346 | biostudies-arrayexpress

Methylome analysis of nerd1-1 mutant seedlings

Project description:DNA methylation profiling in nerd1-1 mutant seedlings 2 biological replicates in dye-swap - MeDIP-chip

2012-12-20 | E-GEOD-35344 | biostudies-arrayexpress

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis

Project description:In eukaryotes, chromatin-based mechanisms superimpose with DNA sequence information to determine the transcriptional output of the genome. Therefore, evaluating the role of chromatin modifications in the regulation of gene expression is key to understand the contribution of chromatin state variations to development. Recent studies identified several transcriptional coactivators that contribute to selectively regulate cellular pathways by coordinating histone H2B monoubiquitination (H2Bub) with other histone modifications. Although H2Bub is present on a large number of genes, loss of H2B monoubiquitination activity was shown to affect RNA steady levels for a small subset of genes and therefore its influence on gene expression is not well understood. In this study we assessed the impact of H2Bub on dynamic expression changes during a rapid developmental tranistion that initiates only when exposing plants to light. This revealed that H2Bub deposition is highly dynamic in a genomic context. Furthermore, plants lacking histone H2B monoubiquitination activity were impaired for rapid changes of RNA levels for a large repertoire of genes, indicating that H2Bub is important for attaining appropriate expression levels /in fine/. Finally, the detection power of the genomic approach has allowed us to define a set of genes impacted by H2Bub dynamics for rapid changes in RNA levels. The purpose of this study was to integrate the genome-wide distribution of H2Bub chromatin mark together with transcriptome profiles of wild-type and /hub1 /mutant plants (accession GSE21922) at three time points during early photomorphogenesis H2Bub epigenome in 5-day-old dark-grown seedlings, H2Bub epigenome in 5-day-old dark-grown seedlings +1h light, and H2Bub epigenome in 5-day-old dark-grown seedlings +6h light 2 biological replicates for each time point in dye-swap - ChIP-chip

2013-03-13 | E-GEOD-36515 | biostudies-arrayexpress

Laccaria-Poplar: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with P. trichocarpa. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N We performed 16 hybridizations (NimbleGen) with samples derived from P.trichocarpa/L.bicolor mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

2014-10-10 | E-GEOD-62225 | biostudies-arrayexpress

Effect of shade and nitrogen content on Arabidopsis Col-0 and cytokinin mutants abcg14 and cypDM

Project description:This project aimed to understand the interplay between light signalling, transzeatin signalling and nitrogen availability on hypocotyl elongation responses. To do so, mRNAseq on shoots was performed, with the following variables studied in all possible combinations: Genotypes: Wild-Type (Col-0), abcg14 (Ko et al., 2014), cypDM (cyp735a1,a2, Kiba et al., 2013) Light quality: White Light (WL, R:FR=2.5), White Light + Far Red light (WL+FR, R:FR=0.25) Nitrate availability: High Nitrate (HN, 10mM KNO3), Low Nitrate (LN, 0.2mM KNO3) Plants were grown for 4 days under WL conditions (16 h light : 8 h dark, PAR=150, 70% humidity, R:FR=2.5 at 20°C) and on the different nitrate conditions. Plants from the WL+FR (R:FR=0.25) samples were treated at ZT 8 for 90min with WL+FR prior the collection of shoots.

2024-09-19 | E-MTAB-13638 | biostudies-arrayexpress

Poplar-Laccaria: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of P. trichocarpa during interaction with the ectomycorrhizal fungus Laccaria bicolor S238N. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation. We performed 32 hybridizations (NimbleGen) with samples derived from Populus trichocarpa control roots and P.trichocarpa mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). All samples were labeled with Cy3.

2014-10-09 | E-GEOD-62172 | biostudies-arrayexpress

Laccaria-Douglas fir: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with Pseudotsuga menziesii. Three time-points were analyzed, two weeks, four weeks and six weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N. We performed 9 hybridizations (NimbleGen) with samples derived from Pseudotsuga menziesii /L.bicolor mycorrhizal root tips. Samples were taken after 2,4 and 6 weeks of interaction (three biological replicates). These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

2014-10-10 | E-GEOD-62226 | biostudies-arrayexpress

QUORUM SENSING IN A METHANE-OXIDIZING BACTERIUM

Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.

2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data