Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of AtATM-dependent X-ray inducible transcript

ABSTRACT: ATM plays an important role in the response of plants to forms of DNA damage that cause DNA double-strand breaks. Arabidopsis ATM has been shown to be important for the transcriptional induction of several DNA repair genes including AtRAD51 (Garcia et al 2003 Plant Cell 15, 119-132). In our experiment we compare the transcript profiles of wild type and mutant plants exposed to 10Gy X-rays (dose rate ~0.8 Gy/min). Plants will be grown on 0.5*MS + 1%sucrose at 22degC under short (9h) day conditions and treated after 5h light. We will irradiate wild type (Col-0) and atatm-3 mutant (N589805) seedlings at growth stage 1.06 and harvest tissue 1h post irradiation. RNA will be isolated using the SV RNA isolation kit (Promega). Comparison of the transcript profiles will then allow AtATM-dependent X-ray inducible transcripts to be identified.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE19252 | GEO | 2009/12/04

SECONDARY ACCESSION(S): PRJNA120795

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification of AtATM-dependent X-ray inducible transcript

Project description:ATM plays an important role in the response of plants to forms of DNA damage that cause DNA double-strand breaks. Arabidopsis ATM has been shown to be important for the transcriptional induction of several DNA repair genes including AtRAD51 (Garcia et al 2003 Plant Cell 15, 119-132). In our experiment we compare the transcript profiles of wild type and mutant plants exposed to 10Gy X-rays (dose rate ~0.8 Gy/min). Plants will be grown on 0.5*MS + 1%sucrose at 22degC under short (9h) day conditions and treated after 5h light. We will irradiate wild type (Col-0) and atatm-3 mutant (N589805) seedlings at growth stage 1.06 and harvest tissue 1h post irradiation. RNA will be isolated using the SV RNA isolation kit (Promega). Comparison of the transcript profiles will then allow AtATM-dependent X-ray inducible transcripts to be identified. 6 samples (3 wild type, 3 mutant) were used in this experiment.

2009-12-03 | E-GEOD-19252 | biostudies-arrayexpress

Expression data from 5 day old Arabidopsis thaliana seedlings

Project description:Upon induction of DNA damage Arabidopsis thaliana plants initiate a transcriptional response program governed by signalling cascades which are activated by the ATM and ATR kinases To analyse if the ATM dependent gene GMI1 (At5G24280) is involved in the regulation of the transcriptionl response, we compared the gene expression profiles of wildtype and gmi1 deficient plants upon gamma-irradiation

2011-04-21 | E-GEOD-23892 | biostudies-arrayexpress

Expression data from 5 day old Arabidopsis thaliana seedlings

2011-04-21 | GSE23892 | GEO

HEC regulation at high ambient temperature gene expression in Arabidopsis thaliana

Project description:The mRNA expression profiles of the WT, hec1hec2, and pifQ were analyzed in 24 hour 22degC and 28degC treated conditions. The gene expression changes was analyzed and compared within 22degC and 28degC.

2021-04-26 | GSE158992 | GEO

Gamma radiation and HZE treatment of seedlings in Arabidopsis

Project description:Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as “collateral” damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment, HZE (1 GeV Fe26+ high mass, high charge, and high energy relativistic particles) and gamma photons, on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs), but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response, although they differ slightly in the timing, degree, and ATM-dependence of the response. The ATM-dependent, DNA metabolism-related transcripts of the “DSB response” were also induced by other DNA damaging agents, but were not induced by conventional stresses. Both Gamma and HZE irradiation induced, at 24 h post-irradiation, ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response, rather than DNA metabolism. In contrast, only HZE-irradiated plants, at 1.5 h after irradiation, exhibited an additional and very extensive transcriptional response, shared with plants experiencing “extended night.” This response was not apparent in gamma-irradiated plants.

2014-09-18 | GSE61484 | GEO

RNAseq for WT, mrg1 mrg2, pif4, and mrg1 mrg2 pif4 plants under different temperature

Project description:To investigate the effect of the interaction between the MRG1/2 and PIF4, here we analysed differentially expressed genes compared to the mutant and wild-type by RNA-seq under different temperature. We performed gene expression profiling analysis using data obtained from RNA-seq of WT, mrg1 mrg2, pif4, and mrg1 mrg2 pif4 plants at 22degC and 28degC.

2024-01-04 | GSE213025 | GEO

SPA regulation of high ambient temperature induced gene expressions in Arabidopsis thaliana.

Project description:The mRNA expression profiles of WT and the quadruple spa mutant spaQ were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes was analyzed and compared within 22degC and 28degC.

2020-09-29 | GSE142354 | GEO

RNA sequence of mouse lung after brain exposed to 10Gy or 10Gy*3

Project description:we reported the lung mRNA change after brain exposed to 10Gy or 10Gy*3 compared to sham ionizing radiation

2021-01-22 | GSE165220 | GEO

The mRNA expression profiles of the hypocotyl and root in WT and hy5

Project description:The mRNA expression profiles of the hypocotyl and root in WT and hy5 were analyzed in 24 hour 22degC and 28degC treated condition. The gene expression changes were analyzed and compared within 22degC and 28degC and in different tissue type (hypocotyl vs root).

2021-03-29 | GSE158939 | GEO

Transcription profiling of atm mutant, adm mutant and wild type whole plants and roots of Arabdiposis after gamma ray irradiation in a time series

Project description:Whole seedlings of wild type (4d) and atm mutants (4d) have been analyzed after a gamma ray irradiation of 0.75h, 1.5h, 3h & 5h (time course). Roots of wt (4d), atm (3d) and atr (4d) mutants have been analyzed after a 1h irradiation.<br><br> Ataxia Telangiectasia Mutated (ATM), encodes a large protein with a phosphatidylinositol 3-kinase (PI3K)-like domain at the C terminus (reviewed by Rotman and Shiloh, 1998). PI3K-related proteins make up a large family of Ser-Thr protein kinases, numerous members of which are involved in the regulation of cell cycle progression, responses to DNA damage, and the maintenance of genomic stability (Hoekstra, 1997). AtATM plays an essential role in meiosis and in the somatic response to DNA damage in plants, similar to the function of ATM in mammals and other eukaryotes.<br>Ataxia telangiectasia-mutated and Rad3-related (ATR) plays a central role in cell-cycle regulation, transmitting DNA damage signals to downstream effectors of cell-cycle progression.

2006-10-30 | E-MEXP-780 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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