Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana strain:T87

ABSTRACT: Genome-wide analysis of transcription start sites and mRNA translation state in Arabidopsis cells

PROVIDER: PRJDB3455 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR029684.fastq.gz	Fastqsanger.gz
	DRR029685.fastq.gz	Fastqsanger.gz
	DRR029686.fastq.gz	Fastqsanger.gz
	DRR029687.fastq.gz	Fastqsanger.gz
	DRR029688.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Transcriptome-wide profiling of RNA N4-cytidine acetylation in Arabidopsis thaliana and Oryza sativa

Project description:Using acRIP-seq, we present transcriptome-wide atlases of ac4C in Arabidopsis thaliana and Oryza sativa. Analysis of ac4C distribution reveals ac4C is enriched near translation start sites in rice while near translation start sites and end sites in Arabidopsis. Further analysis shows ac4C contributes to RNA stability, splicing and translation. We then performed NaCNBH3 treatment and RNA-seq to measure C to T mutation and RNC-seq to measure translation efficiency in Arabidopsis.

2023-06-15 | GSE198286 | GEO

Arabidopsis Nit1 knockout metabolomics

Project description:Glutathione (GSH) is a tripeptide that is implicated in various crucial physiological processes including redox buffering and protection against heavy metal toxicity. GSH is abundant in plants, with reported intracellular concentrations typically in the 1-10 millimolar range. Various aminotransferases can inadvertently transaminate the amino group of the γ-glutamyl moiety of GSH to produce deaminated glutathione (dGSH), a metabolite damage product. It was recently reported that an amidase known as Nit1 participates in dGSH breakdown in mammals and yeast. Plants have a hitherto uncharacterized homolog of the Nit1 amidase. We show that recombinant Arabidopsis Nit1 (At4g08790) has efficient amidase activity towards dGSH. Ablating the Arabidopsis Nit1 gene causes a massive accumulation of dGSH and other marked changes to the metabolome. All plant Nit1 sequences examined had predicted plastidial targeting peptides with a potential second start codon whose use would eliminate the targeting peptide. In vitro transcription/translation assays show that both potential translation start codons were used and subcellular localization of GFP fusions confirmed both cytosolic and plastidial localization. Further, we show that Arabidopsis enzymes convert GSH to dGSH at a rate of 2.8 pmol min-1 mg-1 in vitro. Our data demonstrate that plants have a dGSH repair system that is directed to at least two subcellular compartments via the use of alternative translation start sites.

2018-09-24 | ST001062 | MetabolomicsWorkbench

Changes in translational state from 1 day to 8 day after inoculation in Arabidopsis thaliana T87 cells

Project description:We investigated genome-wide changes in mRNA translation in Arabidopsis thaliana T87 suspension cell cultures which thought to be one of the host materials for bioreactor. Global translational repression was observed in cells of 8 day after inoculation that is thought to be stressful condition by the nutrient deficiency and hypoxia. This suggested the negative effect of the global translational repression on transgene expression. On the other hand, previous study using heat stress showed that some mRNAs were actively translated under such stressful condition, suggesting the existence of mRNA that were actively translated in cells of 8 day after inoculations. To identify mRNAs that escape global translational repression on 8 day and its cis-elements would be the 1st step to make the system for higher transgene expression by the escaping global translational repression. To this end, we subjected polysomal RNA and non-polysomal RNA from sucrose gradient fractionated cell lysates to the co-hybridization on Agilent Arabidopsis 4 Oligo Microarrays. The ratio of signal intensities (polysomal RNA: total RNA) was used as an indicator of the translation state for each transcript.

2013-12-10 | GSE52468 | GEO

Arabidopsis thaliana strain:T87

Project description:Genome-wide analysis of degradation sites in Arabidopsis T87 cultured cell

| PRJDB5913 | ENA

Changes in translational state from 1 day to 8 day after inoculation in Arabidopsis thaliana T87 cells

2013-12-10 | E-GEOD-52468 | biostudies-arrayexpress

Arabidopsis thaliana strain:Columbia-0

Project description:Genome-wide analysis of transcription start sites in Arabidopsis planta

| PRJDB5793 | ENA

Arabidopsis thaliana strain:T87

Project description:Genome-wide analysis of mRNA half-lives in Arabidopsis T87 cultured cell.

| PRJDB6107 | ENA

Arabidopsis thaliana

Project description:Genome-wide identification of transcription start sites in A.thaliana

| PRJDB5045 | ENA

Arabidopsis thaliana

Project description:Increased sucrose levels mediate selective mRNA translation in Arabidopsis

| PRJNA255000 | ENA

Arabidopsis thaliana

Project description:Transcription start site and epigenome analysis of Arabidopsis thaliana T87 cultured cells

| PRJDB9047 | ENA

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