Identification of AtATM-dependent X-ray inducible transcript
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Chris West
PROVIDER: E-GEOD-19252 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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.
2009-12-04 | GSE19252 | GEO
Project description:The Arabidopsis mutant vtc2 is vitamin C-deficient and high light sensitive (Mueller-Moule et al., 2002. Plant Physiol 128: 970-977; Mueller-Moule et al., 2003. Plant Physiol 133: 748-760). Even though the VTC2 gene has been cloned (Jander et al., 2002. Plant Physiol 129: 440-450), its function is still unclear. The goal of this experiment is to learn more about the function of the VTC2 gene by determining differences in the transcriptomes of wild type and the vtc2-1 mutant. In order to differentiate between VTC2 gene-specific differences and vitamin C-induced differences, a second vitamin C-deficient mutant vtc1-1 (Conklin et al., 1996. PNAS 93: 9970-9974) is included in the experiment. The plants will be grown on agar plates in a growth chamber with a 16 hour light (about 40 umol photons m(-2)s(-1))/8 hour dark regime at 20C for 14 days to stage 1.04. Whole plants will be collected and total RNA will be isolated using the Qiagen Rneasy plant mini kit (Qiagen, Hilden, Germany). 9 samples were used in this experiment.
2009-12-05 | E-GEOD-19257 | biostudies-arrayexpress
Project description:The sfr3-1 mutation causes freezing-sensitivity in Arabidopsis thaliana. The mutated gene has been identified by positional cloning and is currently being characterised. The mutant appears normal when grown in the warm (no phenotype has been identified associated with such growth). However, following cold acclimation and subsequent freezing mutant plants are severely damaged whilst wild type plants are not. This suggests that sfr3 is deficient in the cold acclimation process. Micro-array analysis will enable the identification of any transcriptional changes during the cold acclimation process. This information will then be used, together with information obtained by gene characterisation, in order to more fully understand the nature of the sfr3 mutation. 8 samples were used in this experiment.
2009-12-03 | E-GEOD-19254 | biostudies-arrayexpress
Project description:We used three different strains of Pseudomonas syringae pv tomato DC3000 to investigate systemic responses to infection in Arabidopsis and the development of SAR. Wildtype DC3000, the hrpA mutant and DC3000 carrying the avirulence gene avrRpm1 were syringe infiltrated into 4-week-old plants at a concentration of 10e8 cfu/ml. At least 5 leaves per plant were infiltrated and at least 10 plants were pooled for each sample. Systemic, uninfected tissue was then harvested at 8, 12 and 21h after inoculation. Three independent experiments were carried out to give three biological replicates for each timepoint. 27 samples were used in this experiment.
2009-12-09 | E-GEOD-19264 | biostudies-arrayexpress
Project description:MALE STERILITY 35 (MS35/ MYB26) is a R2R3-type MYB transcription factor (Steiner-Large et al., 2003). MS35 is suggested to be a key regulator in the process of lignified secondary thickening in the anther endothecium which provides mechanical force for anther dehiscence (Dawson et al., 1999). The ms35 mutant bears non-dehiscent anthers and thus exhibits a male sterile phenotype. This microarray experiment aims to identify genes controlled by MS35 and thus establish the precise role MS35 plays during anther development. We have demonstrated that MS35 is expressed in the anther during pollen mitotic divisions. Comparisons of gene expression will be carried out between anthers from the Ler.gl (wild-type control) and ms35.gl (mutant) to identify genes with altered expression due to the ms35 mutation. The use of the gl marker will enable a prompt identification of the ms35 mutant amongst the segregating population. The wild-type control line was chosen to be Ler.gl which ensures that the changes of gene expression are not due to the gl mutation. Plants were grown in growth chambers at 22h of daylight (167 umol.m2.sec-1) at 24 C and 2h of night at 24 C. Developmental stages of anthers were defined by bud position and DAPI staining. As soon as the plants showed three fertile or sterile siliques, anther and filaments were collected from both lines at Pollen Mitosis I (PM I), bicellular, and PM II stage, separately. RNA was extracted using RNeasy Mini Kit (Qiagen, USA) and digested with DNase to eliminate genomic DNA contamination. The identified genes will be further analysed using bioinformatics and genomic (knockout) resources that are available for Arabidopsis. 12 samples were used in this experiment.
2009-12-09 | E-GEOD-19267 | biostudies-arrayexpress
Project description:Transcriptional comparison of Arabidopsis thaliana pvip1;pvip2 RNAi double mutants against Col-0 wildtype. Tissue used: whole rosettes of 4-week-old plants grown under short-day conditions (8h light; 20oC). 3 biological replicates for each. Control = Col-0 and mutant = pvip1;pvip2. PVIP = Potyvirus-VPg-interacting protein (Dunoyer et al. 2004 J. Virol. 78: 2301-2309). 6 samples were used in this experiment.
2009-12-10 | E-GEOD-19341 | biostudies-arrayexpress
Project description:Brassinosteroids (BRs) are steroid hormones that are essential for the development of plants. A tight control of BR homeostasis is vital for modulating their impact on various growth responses. However, whilst it is recognized that the rapid adaptation of de novo synthesis plays a key role in adjusting required BR levels, our knowledge of the mechanisms governing feedback control is limited. We identified the transcription factor CESTA as a novel regulator of BR biosynthesis. ces-D was isolated in a screen of Arabidopsis mutants by BR over-accumulation phenotypes. Loss-of-function analysis and the use of a dominant repressor version revealed functional overlap among CESTA and its homologues and confirmed the role of these basic helix-loop-helix proteins in the positive control of BR biosynthetic gene expression. In this experiment we compare the transcriptome of the CESTA mutant to wild-type plants using the Affymetrix ATH1 array. 4 samples were used in this experiment.
2010-07-12 | E-GEOD-20225 | biostudies-arrayexpress
Project description:The objective of this experiment is to identify genes that are regulated by the LRR-receptor-like protein TOO MANY MOUTHS (TMM) to control stomatal precursor (meristemoid) cell fate and behavior. An interesting aspect of the tmm phenotype is that mutant plants overproduce stomata on leaves, but lack stomata entirely on inflorescence stems and in other locations on the plant. Despite the failure to produce mature stomata, mutant stems produce presumptive stomatal precursors through asymmetric divisions. This suggests that normal TMM signaling is required to maintain meristemoid cell fate but not to execute formative asymmetric divisions. Because stem stomata develop in a morphogenetic wave from tip to base, it is possible to harvest tissues that contain meristemoids but not guard mother cells or mature stomata. This provides an opportunity to compare the gene expression profiles of tissues with meristemoids that maintain their cellular identity and ultimately produce stomata (Col gl1), to tissues in which meristemoids form but rapidly lose their cellular identity due to a failure in TMM signaling (tmm-1). Because guard mother cells and stomata are not present in the tissue harvested, genes that change in abundance during these developmental stages will be filtered out. Ultimately we hope to reveal genes that operate downstream of TMM to confer meristemoid cell fate or to provide 'niche factors' suitable for their development into stomata. For analysis, approximately 90 developing inflorescence stem tips were collected and flower buds and meristems removed prior to flash freezing for each replicate sample. The region harvested had been previously determined to contain developing meristemoids but not stomata or guard mother cells by microscopic observation. An identical region was harvested from tmm-1 mutant plants grown at the same time, in the same flat. 4 samples were used in this experiment.
2009-12-03 | E-GEOD-19256 | biostudies-arrayexpress
Project description:In starchless mutants of Arabidopsis, pgm, and wild type, Col0, there are small differences in transcript levels at the end of the day, but large differences at the end of the night. Many of the transcripts of genes involved in biosynthesis and growth are repressed in the pgm mutant (Thimm et al., 2004). It is hypothesized that a transient depletion in sugars at the end of the night inhibits carbon utilization at the beginning of the day (Gibon et al., 2004). In order to test if the same inhibition of transcripts involved in biosynthesis and growth also occurs in starch excess mutants of Arabidopsis, Affymetrix arrays will be generated for WT (Col0), and the following mutants: sex4-3 (Salk 102567), ptpkis2 (Salk 053285), and sex1-3 (Yu et al., 2001). WT, sex4-3, and ptpkis2 plants were grown for 30 days and sex1-3 plants were grown for 36 days. All plants were grown in a growth chamber with a 12 hour photoperiod, quantum flux 100 mol m-2s-1, relative humidity was at least 75%, and a constant temperature of 20oC. Three leaves from 8 different plants of each genotype were harvested using a green safe lamp 0.5 hours before the lights came on in the morning and immediately frozen in LN2. Leaf material was powered using a mortar and pestle and RNA was extracted using a Purescript RNA isolation kit (Gentra Systems, MN, USA). Samples were then treated with DNaseI (Invitrogen, CA, USA). 12 samples were used in this experiment.
2009-12-04 | E-GEOD-19260 | biostudies-arrayexpress
Project description:Aim: To discover the target genes of Golden2-like transcription factors in Arabidopsis. Background: The Golden2-like (GLK) family of transcription factors is essential for proper chloroplast development in several plant species. In Arabidopsis, there are two largely redundant GLK genes, GLK1 and GLK2. Double mutant plants are pale green and reduced in stature. Their most notable chloroplast-related phenotype is impaired thylakoid membrane appression and reduction in steady-state levels of Photosystem II components. GLK proteins group within the GARP family of myb transcription factors; however, the genes they regulate remain unknown. Experimental Design: We have employed a two-component dexamethasone-inducible expression system [1]. An overexpressed fusion protein comprising the glucocorticoid receptor (GR), the lac repressor and the Gal4 activation domain resides in the plant cytoplasm. This protein, termed LHGR-N, enters the nucleus once dexamethasone binds to the GR domain. It then activates transcription from the lac operator promoter sequences present on separate transgenes which carry the cDNA to be induced. Since overexpression of either GLK1 or GLK2 is sufficient to complement the mutant phenotype, we reasoned that induction of expression of GLK1 and GLK2 cDNAs in the glk1;glk2 double mutant background should allow determination of their downstream genetic targets. In the first case, we decided to focus on GLK1 only. Genetic lines: Plants carrying a single copy of the LHGR-N transgene, conferring kanamycin resistance, were crossed with glk1;glk2 double mutant plants. A single homozygous F3 line was selected on the basis of pale green mutant phenotype and kanamycin resistance. This line was transformed with a construct carrying the GLK1 cDNA downstream of six repeats of the lac operator (pOp6) and a single CaMV minimal promoter. This construct confers hygromycin resistance. Transformants were confirmed by PCR and Southern blot, before being selected on the basis of transcript accumulation following induction by dexamethasone. The line with the strongest induction response was chosen for microarray experiments. Tissues: Approx. 100 10-day-old seedlings were grown on MS plates and transferred to 100 ml liquid MS for two further days prior to induction. Whole seedlings were harvested. Treatment: Either a) 10 uM dexamethasone dissolved in DMSO (INDUCED samples) or b) 0.1% v/v DMSO (CONTROL samples). Samples were harvested 4 and 24 hours post-treatment. Separate vessels were used for each time point and treatment. Two complete replicates were performed. Reference1. Craft, J. et al. (2005) Plant J. 41 899-918. 10 samples were used in this experiment.
2009-12-09 | E-GEOD-19265 | biostudies-arrayexpress