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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome profiling of LecRKVI.2 over-expressor plants.

ABSTRACT: The arabidopsis L-type lectin receptor kinase-VI.2 positively regulates bacterial PAMP-triggered immunity. We used microarrays and performed genome-wide transcriptome analysis of LecRKVI.2 over-expressing plants and identified number of upregulated genes involved against bacterial resistance. Total RNA was isolated from 5-week-old Arabidopsis plants for RNA extraction and hybridisation on Affymetrix microarrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: PRASHANT SINGH

PROVIDER: E-GEOD-26646 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome profiling of LecRKVI.2 over-expressor plants.

Project description:The arabidopsis L-type lectin receptor kinase-VI.2 positively regulates bacterial PAMP-triggered immunity. We used microarrays and performed genome-wide transcriptome analysis of LecRKVI.2 over-expressing plants and identified number of upregulated genes involved against bacterial resistance.

2012-03-19 | GSE26646 | GEO

Transcription profiling of Arabidopsis roots to investigate early phosphate-deficiency induced signal changes

Project description:A mutant previously isolated from a screen of EMS-mutagenized Arabidopsis lines, per1, showed normal root hair development under control conditions but displayed an inhibited root hair elongation phenotype upon Pi deficiency. Additionally, the per1 mutant exhibited a pleiotropic phenotype under control conditions, resembling Pi-deficient plants in several aspects. Under Pi deficiency, the accumulation of Pi and iron was increased in the mutant when compared to the wild-type. Inhibition of root hair elongation upon growth on low Pi media was reverted by treatment with the Pi analog phosphite, suggesting that the mutant phenotype is not the result of a defect in Pi sensing. Reciprocal grafting experiments revealed that the mutant rootstock is sufficient to cause the phenotype. Transcriptional profiling of per1 and wild-type plants subjected to short-term Pi starvation revealed genes that may be important for the signaling of Pi deficiency. We conclude that UBP14 function is crucial for adapting root development to the prevailing local availability of phosphate. Experiment Overall Design: Col-0 and per1 mutant plants were grown under control conditions or subjected to phosphate starvation for 10 h

2009-04-18 | E-GEOD-15649 | biostudies-arrayexpress

Iron-deficiency-induced changes in wild type and IRP1overexpressed transgenic Arabidopsis plants

Project description:a novel orphan peptide, IRON-REGULATED PROTEIN1 (IRP1) that is rapidly induced by Fe deficiency and improves growth on Fe-deplete media. In Arabidopsis, ectopic expression of IRP1 affected the activity of several genes involved in Fe acquisition and homeostasis, causing a dramatic increase of Fe in leaves and enhanced seed Fe loading. Heterologous expression of IRP1 in tomato plants resulted in increased Fe levels in fruits. Integration of AtIRP1 into the genome of crop plants may represent a novel strategy for Fe biofortification. wild type Col-0 and transgenic overexpressor IRP1-OE plants were grown under normal conditions or subjected to and iron-starvation for 3 days. Roots and shoots were collected with 3 biological replicates.

2014-10-10 | E-GEOD-51692 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild-type and lwd1lwd2 double mutant to investigate the role of LWD1 and LWD2 in Arabidopsis photoperiod regulation

Project description:Transcriptome analysis has revealed a light-regulated WD (tryptophan and aspartate)-containing protein, LWD1. LWD1 and LWD2 share greater than 90% amino acid sequence homology. The lack of phenotype changes in the lwd1 or lwd2 single mutant implies that the proteins function redundantly. The lwd1lwd2 double mutant, however, has an early flowering phenotype under both long-day (LD) and short-day (SD) conditions. Functional complementation experiment revealed that LWDs are indeed responsible for the defect in photoperiod sensing in lwd1lwd2 double mutant plants. The expression of LWD1 exhibits a diurnal pattern and peaks before dawn. The period length of oscillator (CCA1, LHY, TOC1 and ELF4) and output (CCR2 and CAB2) genes in the lwd1lwd2 double mutant is significantly shorter than that in wild-type Arabidopsis under free running condition. Under entrainment conditions, the expression phase of oscillator (CCA1, LHY, TOC1 and ELF4) and output (GI, FKF1, CDF1, CO and FT) genes shifts ~3 hr forward in the lwd1lwd2 double mutant. Our data indicated that the early flowering phenotype in lwd1lwd2 plants is contributed by the significant phase shift of CO and, therefore, an increased expression of FT before dusk under SD conditions. Our data imply that LWD1/LWD2 proteins function in close proximity to the circadian oscillators for the regulation of photoperiod sensing. Experiment Overall Design: Two biological replicates were performed to examine the differential gene expression between wild-type and lwd1lwd2 double mutant. The plants were grown under 12 h L/ 12 h D for 31 days before harvesting their above ground tissues at ZT5-9.

2008-10-26 | E-GEOD-11762 | biostudies-arrayexpress

Iron-deficiency-induced changes in wild type, ubc13A and cucumber CsUBC13 overexpressed Arabidopsis thaliana roots

Project description:CsUBC13 was identified via proteomics from iron starvation treated Cucumber root. ubc13A is an ABRC seed stock (CS51269). CS851269 was purchased from ABRC and confirmed as homozygous Atubc13A knock-out T-DNA mutant. We generated transgenic arabidopsis with ectopic expression of CsUBC13 gene under control of the cauliflower 35S promotor. Both genotypes and Col-0 were used to investigate the transcriptional response to Iron (Fe) deficiency. Wild type Col-0, ubc13A and transgenic overexpressor OE were grown under normal and iron-deficiency conditions. Roots were collected with 3 biological replicates.

2009-07-07 | E-GEOD-16964 | biostudies-arrayexpress

Heat stress UNR

Project description:To identify transcripts that are regulated by putative transcriptional co-activators, WT (Col) and KO of heat responsive transcriptional co-activator (Multiprotein Bridging Factor 1c) in Arabidopsis were subjeted to heat stress. These plants were compared to find transcripts that are regulated by the transcriptional co-activator during heat stress.

2011-06-09 | E-MEXP-2760 | biostudies-arrayexpress

Early Iron Deficiency Induced Changes in Arabidopsis Roots

Project description:Due to limited bio-availability of Fe, plants evolved adaptive alterations in development regulated at the transcriptional level. We investigated the early transcriptional response to Fe deficiency. A hydroponic system was used that allows bulk transferring of plantsand rapid Fe removal with little mechanical damage to the root systems.

2009-03-13 | E-GEOD-15189 | biostudies-arrayexpress

Transcription profiling of 148 Arabidopsis recombinant inbred lines treated with Silwet solution to develop genetic markers and derive high-density haplotypes

Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We surveyed recombinant inbred lines (RILs) from a population derived from a cross of inbred Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) in order to map e-QTLs controlling ELPs. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 28 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for 148 RILs, plus replicated Bay-0 and Sha control samples grown at the same time as the RILs. These GeneChips were used to develop genetic markers and derive high-density haplotypes for the RILs

2007-01-10 | E-TABM-62 | biostudies-arrayexpress

Transcription profiling of Arabidopsis recombinant inbred lines treated with salicylic acid or a control solution to map expression QTLs controlling expression level polymorphisms

Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We surveyed recombinant inbred lines (RILs) from a population derived from a cross of inbred Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) in order to map e-QTLs controlling ELPs. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 28 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the SA-treated samples for 211 RILs, plus replicated Bay-0 and Sha control samples grown at the same time as the RILs. The control (Silwet-treated) samples were submitted as E-TABM-126. Normalized data is not provided here as the normalization step was included in the data statistical analsyses - for more information please contact the experiment provider.

2009-07-17 | E-TABM-518 | biostudies-arrayexpress

Genome-wide maps of AGO1-bound small RNA in Arabidopsis leaves

Project description:We report flg22 regulate the accumulation of AGO1-bound small RNA in arabidopsis. We find that a number of miRNAs are up- or down-regulated by flg22, a well-studied PAMP. Examination of AGO1-bound small RNAs with or without flg22 treatment.

2010-02-25 | E-GEOD-20448 | biostudies-arrayexpress

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