Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression analysis of Arabidopsis thaliana wild-type Col-0 and selected RNA silencing mutant plants

ABSTRACT: Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE60508 | GEO | 2014/08/20

SECONDARY ACCESSION(S): PRJNA258445

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression analysis of Arabidopsis thaliana wild-type Col-0 and selected RNA silencing mutant plants

Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press). A twelve chip study using total RNA recovered from three week-old plants grown on Murashige Skoog sucrose agar. The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2) and nrpe1 (2) respectively. Each array contains 60-mer probes targeting 39,042 genes (TAIR 9.0) with 4 probes per gene.

2014-08-20 | E-GEOD-60508 | biostudies-arrayexpress

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [RNA-seq]

Project description:The evolutionally conserved COMPASS complexes are responsible for the catalyzation of H3K4 methylations. Recently, three types of COMPASS complexes which contains histone methyltransferases ATX1/2, ATX3, or ATX4/5 were identified in Arabidopsis. Here, we report the ATX proteins are essential for the survival of Arabidopsis. By RNA-seq and chromatin immunoprecipitation (ChIP-seq) analysis, we found ATX1/2-, ATX3-, and ATX4/5-containing COMPASS complex redundantly regulate gene expression and H3K4me3 modifications. In addition to the developmental-related genes, we found the expression of DNA methylation-related genes were also regulated by the COMPASS complexes. The transcript and H3K4me3 levels at the RdDM pathway genes (NRPE1, DCL3, IDN2, FDM2) and at the DNA demethylase encoding genes (ROS1, DML2, DML3) were down-regulated in atx1/2/4/5 mutants. Via bisulfate sequencing, we found the atx1/2/4/5 showed hypermethylation at CG and CHG contexts whereas the hypomethylation at CHH contexts. By comparing the differentially methylated regions (DMRs) in atx1/2/4/5 with that in ros1;dml2;dml3 (rdd) and in nrpe1, a large part of overlapping DMRs were identified. Based on these results and other findings, we propose that the hypermethylation in CG and CHG is partially caused by the down-regulation of ROS1/DML2/DML3, and the hypomethylation in CHH is mainly caused by the down-regulation of NRPE1. Furthermore, we revealed that the COMPASS complexes also play a redundant role in regulating the transcription of transposable elements (TEs). This study extends our knowledge about the function of COMPASS in plant development and illustrate the important roles for COMPASS complexes in the regulation of DNA methylation and TEs transcription.

2022-11-14 | GSE206687 | GEO

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [ChIP-seq]

2022-11-14 | GSE206685 | GEO

COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [Bisulfite-seq]

2022-11-14 | GSE206683 | GEO

Highly integrated epigenome maps in Arabidopsis - transcriptome sequencing

Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput transcriptome sequencing Transcriptome sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

2008-04-20 | E-GEOD-10968 | biostudies-arrayexpress

Highly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing

Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress

Highly integrated epigenome maps in Arabidopsis - small RNA sequencing

Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput small RNA sequencing Small RNA sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.

2008-04-20 | E-GEOD-10967 | biostudies-arrayexpress

MethlyC-Seq of Col-0 (wild type, WT), nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT, nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant

2016-11-01 | GSE72280 | GEO

Active DNA demethylation regulates MAMP-triggered immunity in Arabidopsis

Project description:We found that active DNA demethylation is required for MAMP-triggered immunity to bacteria pathogen. Triple mutant plants deficient in ROS1, DML2, and DML3 (RDD) exhibited compromised immune responses such as induction of immune genes .

2022-06-20 | GSE156608 | GEO

Whole genome bisulfite sequencing of two/three-week-old Arabidopsis thaliana plants of the genotypes Col-0, nrpe1-11 and ros1-4.

Project description:This study used the mutants nrpe1-11 and ros1-4 to assess the impact of RNA-directed DNA methylation (RdDM) and ROS1 on the Arabidopsis thaliana (ecotype Col-0) methylome.

2022-11-07 | GSE199625 | GEO

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