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Transcriptional regulation of ROS controls the transition from proliferation to differentiation in the root

ABSTRACT: We isolated the meristematic and elongation zones of Col-0, upb1-1 mutant and 35S::UPB1-3YFP/upb1-1 plants by micro-dissection and extracted RNA from each section independently. To identify genes that might mediate UPB1 function we conducted a series of microarray experiments. The spatial distribution of the UPB1 protein suggested that it might exert a different effect on gene expression in the meristematic and elongation zones. Therefore, we isolated the meristematic and elongation zones by micro-dissection and extracted RNA from each section independently.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE21876 | GEO | 2010/11/12

SECONDARY ACCESSION(S): PRJNA126839

REPOSITORIES: GEO

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Transcriptional regulation of ROS controls the transition from proliferation to differentiation in the root

Project description:We isolated the meristematic and elongation zones of Col-0, upb1-1 mutant and 35S::UPB1-3YFP/upb1-1 plants by micro-dissection and extracted RNA from each section independently. To identify genes that might mediate UPB1 function we conducted a series of microarray experiments. The spatial distribution of the UPB1 protein suggested that it might exert a different effect on gene expression in the meristematic and elongation zones. Therefore, we isolated the meristematic and elongation zones by micro-dissection and extracted RNA from each section independently. Total RNA was isolated from approximately 60 meristem- and elongation zones of Col-0, upb1-1 and 35S::UPB1-3YFP #2 6 day old plants. Two biological replicates were performed for each experiment.

2010-11-12 | E-GEOD-21876 | biostudies-arrayexpress

Gene expression and H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants

Project description:This SuperSeries is composed of the following subset Series: GSE24464: Expression analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants GSE24474: H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants Refer to individual Series

2011-04-20 | E-GEOD-24507 | biostudies-arrayexpress

Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles [RNA-seq]

Project description:The root apex is an important section of the plant root, involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging, especially when the samples are limiting and precious, such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study.To understand the gene expression profiles of the root apex, Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm, root cap and meristematic zone) and Zone-II (1.5 mm, transition, elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq.Both the techniques, arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition, 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays. Single root tip zones can be used for full transcriptome analysis; further, the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small, rare samples.

2018-10-29 | GSE115554 | GEO

Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles [microarray]

2018-10-29 | GSE115486 | GEO

A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar

Project description:Paired-end RNA-Seq libraries were constructed for three root sections of the roots of barley cv. Clipper, and landrace Sahara, grown under control and salt-treated (100 mM NaCl) conditions on agar plates in quadruplicate. Experiments were conducted in a temperature-controlled growth cabinet at 17 C in the dark. After three days of germination, seminal roots were dissected according to the following steps: A 1.5 mm long section marked Zone 1 (meristematic zone) was taken from the root tip. A second section (Zone 2) was dissected from the elongation zone up to a third section, Zone 3 (maturation zone), which was excised at the point of visible root hair elongation up to 34 of the entire root. Four biological replicates were generated for each sample in four separate experiments totaling 48 samples. All RNA-seq libraries were constructed and paired-end sequenced (100 bp) on an Illumina HiSeq 2000 system at the Australian Genome Research Facility (Melbourne, Australia).

2016-06-27 | E-MTAB-4634 | biostudies-arrayexpress

Global gene expression profiling in mouse plasma cell tumor precursor and bystander cells revels potential intervention targets for plasma-cell neoplasia

Project description:We extracted nascent plasma cell tumor (PCT) cells from within inflammatory granulomas (OG) isolated from intraperitoneal pristane-injected BALB/c.iMyc Eμ mice at five different time points during tumor progression. We used laser capture micro-dissection to collect incipient PCT cells and analyzed their global gene expression on Affymetrix Mouse Genome 430A microarrays. Two independent studies were performed with different sets of mice

2011-12-02 | GSE34078 | GEO

Root Meristem Growth Factor 1 (RGF1) controls root meristem size through reactive oxygen species (ROS) signaling

Project description:Purpose: Although five receptors of RGF1 have recently been identified, the downstream signaling mechanism remains unknown. The goal of this study is to elucidate signaling events following RGF1 action. Methods: mRNA profiles of the root meristematic zone from Arabidopsis seedlings with or without RGF1 treatment were generated by deep sequencing, in triplicate. The sequence reads were analyzed using Tophat and DESeq2. The mutants of selected differentially expressed genes were generated for phenotyping. Results: Our study uncovered a series of signaling events following RGF1 action. The RGF1-receptor pathway controls distribution of reactive oxygen species (ROS) along the developmental zones of the Arabidopsis root. We identify a novel transcription factor, RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), which plays a central role in mediating RGF1 signaling. Manipulating RITF1 expression leads to redistribution of ROS along the root developmental zones. Changes in ROS distribution, in turn, enhance the stability of the PLETHORA2 (PLT2) protein, a master regulator of root stem cells. Conclusions: Our study clearly depicts a signaling cascade initiated by RGF1 and links the RGF1 peptide to ROS regulatory mechanisms.

2019-10-15 | GSE108730 | GEO

affy_dormance_mrnaoxidized_sunflower-Molecular mechanisms of seed dormancy release: transcriptome evolution and ROS signalling during sunflower seed after-ripening.

Project description:affy_dormance_sunflower - affy_dormance_mrnaoxidized_sunflower - We focus our research on the release of embryonic dormancy in sunflower seeds and more precisely on the molecular mechanisms controlling seed dormancy release during dry after-ripening. Our data show an increase of ROS during dormancy release associated with an increase of stored mRNA oxidation during after-ripening as shown with determination of the RNA oxidation marker : 8-hydroxyguanosine (8OHG) To assess to role of mRNA oxidation in this process, we isolated 8OHG-containing mRNA to identify oxidized transcript using microarray analysis.-The samples compared are the following: 1) 8OHG containing mRNA isolated from total RNA extracted from a population of 100 embryonic axis of dry dormant seed (Dox) ie. Seed which have been frozen at -30°C after harvest to keep dormancy 2) 8OHG containing mRNA isolated from total RNA extracted from a population of 50 embryonic axis from dry non dormant ie. Seeds which have been after-ripened (stored) at 70% RH during 2 month (NDox) Replicates correspond to different batches of seeds from the same harvest, which have been treated (after ripened) independently and from which the 8OHG containing fraction have been isolated independently.

2011-07-20 | GSE23048 | GEO

Gene expression in the islets of 12 wk old Non-Obese Diabetic (NOD) mice and healthy control NOD.B10 mice

Project description:Gene expression in the islets of NOD and NOD.B10 mice at 12 weeks of age, prior to the onset of destructive insulitis. The pancreata of NOD and NOD.B10 mice (n=6) were frozen and islets were isolated by laser capture microdissection. Cryosections (8 M-NM-<m) were cut and stained using the Arcturus HistoGene Frozen Section Staining kit (Applied Biosystems) and laser dissection was performed using the Leica AS LMD and the Leica IM 1000 Image Manager Basic software. Sections from at least 40 individual islets were collected and RNA was extracted using the RNeasy micro kit (Qiagen). RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Reagent Kit (Agilent). Samples were preamplified using the TrueLabeling-PicoAMP kit (SA Biosciences), post-labeled with Cy5 and run against a Cy3-labeled mouse Universal RNA control (SA Biosciences). Microarrays were performed using the Whole Mouse Genome Microarray Kit, 4M-CM-^W44K 2-color arrays (Agilent Technologies).

2013-04-10 | E-GEOD-45897 | biostudies-arrayexpress

Effects of exendin-4 in Brunner's glands of male GLP-1R-/- and wild-type control mice

Project description:To gain insight into the biological functions of the highly expressed GLP-1R in Brunner’s glands, transcriptome analyses were conducted in male GLP-1R-/- and wild-type control mice. Analyses were performed 6 hours after a single s.c. dose of exendin-4 (1.0mg/kg s.c.), following 18 hours of two doses of exendin-4 (1.0 mg/kg s.c., administered at 0 and 9 hours), and in untreated controls. Brunner’s glands were isolated by laser capture micro dissection and extracted total RNA was used for microarray profiling.

2016-07-01 | GSE80119 | GEO

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