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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of a N-6 adenosine methylation deficient plant

ABSTRACT: The embryo lethal adenosine methylase tDNA knockout line SALK_074069 was partially complemented with its cDNA driven by the embryo specific ABI3 promoter (A6 lines). The plants have reduced adenosine methylation and show pleiotropic phenotypes. Rosette leaves were harvested from 3 week old plants, both wild-type and mutant plants in triplicate and analysed using the Affymetrix ATH1 array. The 3rd to 6th rosette leaves were harvested in triplicate from 3 week old wild-type and mutant plants (A6). Total RNA was extracted and hybridised to the Affymetrix ATH1 array.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Neil Graham

PROVIDER: E-GEOD-34924 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of a N-6 adenosine methylation deficient plant

Project description:The embryo lethal adenosine methylase tDNA knockout line SALK_074069 was partially complemented with its cDNA driven by the embryo specific ABI3 promoter (A6 lines). The plants have reduced adenosine methylation and show pleiotropic phenotypes. Rosette leaves were harvested from 3 week old plants, both wild-type and mutant plants in triplicate and analysed using the Affymetrix ATH1 array.

2012-05-02 | GSE34924 | GEO

wt and opr3 control and systemic wounding

Project description:wt plants (ws) and opr3 mutant plants were wounded Half of the rosette leaves of 6 weeks old plants were wounded by clamping a tweezers across the midvein. RNA was extracted from control and systemic leaves 2 h after wounding, and was subject to affymetrix ATH1 chip.

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Analysis of the Aloe vera transcriptome using the Affymetrix ATH1 GenChip

Project description:The Aloe vera transcriptome was analysed by hybridising triplicate samples of root and leaf tissue to the Affymetrix Arabidopsis ATH1 array. In total, 7 samples were hybridised to the array. Samples consisted of 1 genomic DNA, and triplicate samples of leaf and root RNA.

2011-03-26 | E-GEOD-24389 | biostudies-arrayexpress

wt and opr3 control and systemic wounding

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DCL4 Functional Analysis

Project description:Rosette leaves (5-8) and inflorescence stages (1-12) from dcl1-7, rdr6-15, and dcl4-2 mutants, involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays. Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and trans-acting siRNAs). Keywords: other

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Transcription profiling of Arabidopsis rosette leaves and inflorescences from dcl1-7, rdr6-15 and dcl4-2 mutants

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Genome-wide identiﬁcation of circular RNAs in Arabidopsis thaliana

Project description:To exlore more circRNAs involved in Arabidopsis thaliana, we deeply sequenced 14 samples including whole plants from four developmental stages (rosette leaves > 1 mm in length; rosette growth complete; 50% of flowers to be produced have opened; first silique shattered), aerial part of plants from four stress treatments (control, drought, salinity and heat), five organs (roots, stems, leaves, flowers and siliques) and a mixed sample from whole plants across the lifespan (cotyledons emergence, rosette leaves﹥1 mm, rosette growth complete, first flower open, flourishing florescence, first silique shattered, senescence). The total RNA was purified by rRNA-depletion and linear RNA removal with RNAseR, and paired-end (PE) sequenced by Illumina HiSeq 2500 (read length, PE125, the mixed sample) and Illumina Hiseq X Ten (read length, PE150, 13 independent samples) platforms. We obtained 181.97 Gb raw data (151.37 Gb from 13 samples and 30.6 Gb from a mixed sample) and identified 5861 circRNAs with expression quantity. We annotated the parent genes of these circRNAs and predicted their target sites of microRNAs.

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Comparison of gene expression in Arabidopsis trichome between gtl1-1 mutant and wild type

Project description:Total RNA from trichomes of fifth and sixth rosette leaves of three-week-old wild-type and gtl1-1 mutants (Figure 3B) were extracted. We found a total number of 1,759 genes, corresponding to 1,694 probes on the ATH1 chip, that show differential expression of at least 1.3-fold. Out of these 1,694 genes, 47.2% are positively regulated and 52.8% are negatively regulated by GTL1.

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Root and rosette leaves transcriptome of Arabidopsis Col-0 and nrt1.5 mutant

Project description:Differentially regulated genes in rosette leaves and roots of hydroponically grown Arabidopsis thaliana Col-0 and nrt1.5-5 mutant plants were identified by microarray analyses.

2017-02-28 | GSE60975 | GEO

Transcription profiling of Arabidopsis thaliana (Ler) rosette leaves treated with paraquat (methyl viologen)

Project description:We used microarrays to detail Arabidopsis gene expression in response to paraquat, a herbicide that acts as a terminal oxidant of photosystem I that in the light leads to the enhanced generation of superoxide and hydrogen peroxide inside plastids. Within a few hours after paraquat treatment changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by another reactive oxygen species, singlet oxygen. Experiment Overall Design: Arabidopsis thaliana rosette leaves were harvested 1, 2, and 4 h after spraying either with a solution of 20 microM paraquat (methyl viologen, Sigma) in 0.1% Tween or with Tween alone for RNA extraction and hybridization on Affymetrix ATH1 microarrays. Plants were grown on soil for 3 weeks under continuous light at 90 mmol. m-2 . s-1. For each sample, the rosette leaves of five to six 3-week-old plants (before they start bolting) were collected for RNA extraction. Total RNAs from two separate biological experiments were pooled for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.

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