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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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE34924 | GEO | 2012/05/02

SECONDARY ACCESSION(S): PRJNA150149

REPOSITORIES: GEO

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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. 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.

2012-05-01 | E-GEOD-34924 | biostudies-arrayexpress

mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana [smallRNAs]

Project description:In order to assess the possible effects of m6A on miRNA biogenesis we performed small RNA (sRNA) sequencing to compare their levels in WT Col-0 plants to those in mutant lines with severely reduced m6A levels. The reduced mta line contains MTA cDNA under the ABI3 promoter in MTA null mutant background (ABI3:MTA) and ABI3 being an embryo specific promoter rescues the embryo lethal phenotype of MTA knockout while keeping the levels of MTA in mature plants severely low34. sRNAs isolated from 4 week old WT and mta plants were used to make libraries that were sequenced using HiSeq® (Illumina) and the results were analyzed using NOISeq package in R-Studio.

2020-09-21 | GSE122526 | 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.

2010-12-01 | GSE14332 | GEO

What is the transcriptomic contrast between a TDNA-mutant and its respective wild-type from young Arabidopsis rosette?

Project description:ra15-07_burxcol_465 - burxcol-465 - What is the transcriptomic contrast between a TDNA-mutant and its respective wild-type from young rosette grown in precisely-controlled conditions on our phenotyping robot (Phenoscope)? - The candidate gene (AT1G36310) was identified through QTL mapping and cloning for rosette leaf growth trait in a Bur x Col RIL set. It corresponds to a medium effect on growth and a major effect on other traits (leaf colour and pigments). We are now exploiting an independent TDNA-insertion line (SALK_135308) in the Col-0 background) to study its effect in a simple genetic context. This is a simple comparison between homozygous T-DNA (2 lines) and their respective WT (2 lines).

2017-02-01 | GSE93513 | GEO

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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Adenosine induced gene expression

Project description:HCT116 cells are treated by adenosine (4 mM) for 6 hours and then using total RNA for sequencing analysis to evaluate adenosine induced gene expression.

2023-11-29 | GSE216006 | GEO

wt and opr3 control and systemic wounding

2010-12-01 | E-GEOD-14332 | biostudies-arrayexpress

Rat MeDIP Array, naïve, epileptic, and adenosine treated

Project description:Epilepsy causes altered gene expression; transient adenosine treatment inhibits progression of epileptogenesis Hippocampus of epileptic rat is hypermethylated compared to naïve; adenosine treatment causes hypomethylation Metylation state in epileptic rats (9 weeks post kainic acid induced status epilepticus) was compared to naïve (untreated) rats and epileptic rats treated with adenosine for 5 days

2013-09-05 | E-GEOD-45932 | biostudies-arrayexpress

Adenosine-treated endothelial progenitor cells

Project description:The goal of this study was to investigate the effects of the cardioprotective nucleoside adenosine on gene expression in early and late endothelial progenitor cells. Adenosine mod

2011-01-29 | GSE26744 | GEO

Gene regulation by the seed maturation master regulators, LEC1, LEC2, FUS3 and ABI3 [set 2]

Project description:During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reserve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed. Developing seeds were dissected from the siliques of the abi3-6 homozygous plants or the respective wild type plants (Col-0) at 12 and 16 days after flowering. Seeds samples were obtained from triplicate batches of plants and used for RNA preparation.

2014-10-01 | E-GEOD-61685 | biostudies-arrayexpress

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