Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of expression in Arabidopsis mutant tdt-1 and wild type

ABSTRACT: The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Keywords: Genetic modification affect on gene expression

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE7359 | GEO | 2007/07/31

SECONDARY ACCESSION(S): PRJNA100431

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling of Arabidopsis mutant tdt-1 and wild type

Project description:The object of this study was to explore whether the loss of mRNA decapping in the Arabidopsis mutant tdt-1 resulted in global dfferences of RNA profiles, as compared to wild type. Experiment Overall Design: In this experiment we compared expression in tdt-1 and wild type 3 day whole seedlings. We performed three biological replicates, in which one experiment was dye-swapped.

2008-06-15 | E-GEOD-7359 | biostudies-arrayexpress

Next Generation Sequencing of T regulatory cells (GFP+, dTomato+) and ex-T regulatory cells (GFP-, dTomato+) harvested from lymph nodes of bone marrow chimeras (50% Foxp3GFP-tdT or Foxp3GFP-Fth/-tdT and 50% C57BL/6 bone marrow into Rag2-/- recipients)

Project description:Purpose: To address whether FTH regulates gene expression in TREG cells, irrespective of bystander inflammation. For this, we compared the gene expression profile of TREG and Ex-TREG cells sorted from the lymph nodes of mixed BM chimeras Results: Using an optimized data analysis workflow, we mapped an average 30.14 million sequence reads per sample to the mouse genome (build mm39) and identified 34,321 transcripts in the mRNA of Treg and Ex-Treg cells from mixed bone marrow chimeras. Differential gene expression was performed using the DESeq2 R package (v.1.32) and gene expression was modeled by genotype and condition. Differentially expressed genes were considered for genes with an adjusted p-value<0.05 and an absolute log2 fold change>0. Conclusions: Analysis of RNAseq data showed that Fth deletion in TREG cells (CD45.2+GFP+tdT+) developing from the BM of Foxp3GFP-Fth∆/∆-tdT mice, up-regulated 149 genes and down-regulation of 96 genes, compared to TREG cells from control Foxp3GFP-tdT mice. Ex-TREG cells (CD45.2+GFP-tdT+) up-regulated 90 genes and down-regulated 36 genes. The genes regulated in TREG and ex-TREG cells originating from the BM of Foxp3GFP-Fth∆/∆-tdT vs. Foxp3GFP-tdT mice were associated with the oxidative stress response regulated by NRF2 . This suggests that FTH exerts cell-autonomous control of TREG cell redox homeostasis, irrespective of bystander inflammation.

2024-01-29 | GSE226032 | GEO

The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [RNA-seq]

Project description:Cytoplasmic mRNA decay occurs through several pathways, but the contributions of these decay pathways to the degradation of specific mRNAs, and interactions between the pathways, are not well understood. We carried out a genome-wide analysis of mRNA decay rates using wild-type Arabidopsis and mutants with defects in mRNA decapping and SOV/DIS3L2. Decay rates and contributions of decapping and SOV to decay were estimated for 18,674 mRNAs using maximum likelihood modeling. Most mRNAs decayed by multiple pathways, few mRNAs degraded exclusively by mRNA decapping or SOV, and specific codon usage was linked to decay rates. Unexpected faster decay of transcripts in some genotypes was found to be independent of siRNAs; instead the data suggested an RNA buffering-like phenomenon in Arabidopsis, and that VCS (decapping) is essential for both this process and the decay of very unstable mRNAs.

2018-01-26 | GSE86359 | GEO

The Cytoplasmic mRNA Decay Landscape of Arabidopsis Seedlings [small RNA-seq]

2018-01-26 | GSE86360 | GEO

Arabidopsis thaliana Wild-type vs. mutant sdg2

Project description:Transcriptional profiling of Arabidopsis wild-type (Col0) control seedlings with corresponding mutant seedlings is performed using Aligent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K).

2017-02-09 | GSE39898 | GEO

Arabidopsis thaliana Wild-type vs. mutant (PcG)

Project description:Transcriptional profiling of Arabidopsis wild-type (Col0) control flower buds or seedlings with corresponding mutant flower buds or seedlings is performed using Aligent's Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K).

2020-02-01 | GSE94731 | GEO

Gene expression comparison between Arabidopsis wild type (Col) and stomata mutant

Project description:As the gate for gas exchange and water vapor, stomata play an essential role in plant development. It has been a long time that many research focus on how the opening and closing of stomata is controlled. Until recently, studies on how stomata are formed in Arabidopsis just emerge. With a cluster of guard cells in one stomate in flp-1/myb88 mutant, it will be great interest to understand how FLP/MYB88 control stomata development. By taking advantaging of microarray technology, we intend to study a set of genes regulated by FLP/MYB88, which will facilitate us to better explore the biological functions of FLP/MYB88 in stomata development, even in the biotic or abiotic stresses.

2009-09-01 | GSE12911 | GEO

Decapped mRNAs during Arabidopsis Early Flower Development

Project description:The composition of the transcriptome is regulated by both mRNA synthesis and degradation. One route for mRNA decay is through 5’ decapping, which can be initiated by decapping enzymes and small RNAs. Although decapped RNAs are an important intermediate for mRNA decay, their identity and abundance have never been studied on a large scale. Here we present an experimental method for transcriptome-wide profiling of decapped mRNAs. We applied the method to study the prevalence of decapped transcripts during the early stages of Arabidopsis thaliana flower development. Decapped transcripts were identified for the majority of expressed genes, although at different levels. By comparing decapped RNA levels with steady-state overall transcript levels, our study provides evidence for widespread decapping-mediated mRNA degradation control in numerous biological processes and for genes of varied molecular functions, implying that mRNA decapping is a dynamically regulated process. Sequence analyses identified structural features of transcripts and cis-elements that were associated with levels of decapping.

2008-10-10 | GSE12043 | GEO

Arabidopsis thaliana

Project description:Comparison of expression in Arabidopsis mutant tdt-1 and wild type

| PRJNA100431 | ENA

Transcriptional Analysis of lsm1a lsm1b Arabidopsis mutant.

Project description:Characterization of the lsm1a lsm1b transcriptional profile. LSM1 protein is involved in RNA decay through decapping facilitation. The performed array help us to understand the transcription level alterations produced by the absence of LSM1.

2013-01-16 | GSE39630 | 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