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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Arabidopsis thaliana vegetative part: Col-0 vs. shr scl23 scr triple mutant

ABSTRACT: Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis. Two-condition experiment: Col-0 vs. shr scl23 scr triple mutant. Biological replicates: 2 WT vs. triple mutant replicates, 2 WT vs. triple mutant replicates dye-swap replicates.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Eun Kyung Yoon

PROVIDER: E-GEOD-41478 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Arabidopsis thaliana vegetative part: Col-0 vs. shr scl23 scr triple mutant

Project description:Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis.

2012-10-11 | GSE41478 | GEO

The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root

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The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root

Project description:Asymmetric division of cortex/endodermal initials (CEI) in the Arabidopsis root generates two layers of ground tissue and is controlled by a finely orchestrated interplay between the transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR). To understand the dynamics of the SHR/SCR regulatory network we performed microarray time course experiments using inducible versions of SHR and SCR and examined their transcriptional effects specifically in the ground tissue. Keywords: SHR and SCR time course and CEI cell-type analyses We performed a time course analysis (TC data set) of the ground tissue (sorted J0571 enancher trap) after transfer either SHR or SCR inducible plants to Dex containing plates 0, 1, 3, 6 and 12 hours. We sorted for CEI cells using the pCYCD6::GFP marker line. Seedlings were grown for 5 days. SHR and SCR inducible plants were transfer to 1microM Dex MS plates. J0571 and CYCD6 sorted fluorecent cells were harvested for RNA extraction.

2010-07-19 | E-GEOD-15876 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Arabidopsis thaliana vegetative part: Col-0 vs. shr scl23 scr triple mutant

| PRJNA177123 | ENA

Expression changes by Endodermal PIF1: SCR:PIF1/pifQ transgenic plant vs. pif1pif3pif4pif5 (pifQ) mutant

Project description:Transcriptional profiling of dark-grown Arabidopsis seedlings comparing SCR:PIF1/pifQ transgenic plant with pif1pif3pif4pif5 quadruple mutant (pifQ). Seedlings were grown under dark condition for 2.5 days. Goal was to determine the effects of endodermal PIF1 in dark-grown seedlings. Two-condition experiment, SCR:PIF1/pifQ vs. pifQ Biological replicates: 3 pifQ replicates, 3 SCR:PIF1 replicates.

2016-08-01 | E-GEOD-71918 | biostudies-arrayexpress

Arabidopsis Col vs vim1,2,3 triple mutant

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2014-10-02 | E-GEOD-55956 | biostudies-arrayexpress

Genome-wide analysis of PHABULOSA targets in Arabidopsis root meristem

Project description:We report the discovery of a root growth program in Arabidopsis that is independent of a functional quiescent center (QC). In this regulatory program, PHABULOSA (PHB), posttranscriptionally regulated by SHR and SCR, plays a central role. In phb shr and phb scr mutants, root meristem/growth activity recovers significantly. Interestingly, this recovery does not accompany the resurgence of QC cells. PHB regulates apical root growth in stele cells of the root meristem, located proximal to the QC. Our genome-wide investigation suggests that PHB exerts its influence on root growth by regulating auxin-cytokinin homeostasis. Apical root growth was restored when cytokinin levels were genetically reduced in the shr mutant. Conversely, when miRNA-resistant PHB was expressed in the root stele cells, apical root growth and meristem functions were significantly inhibited without blocking the QC identity. Taken together, our investigation reveals two mechanisms through which SHR regulates root growth and stem cell activities: one is to specify and maintain the QC and the other is to regulate the proximal meristem activity through PHB and cytokinin. In this regulation, QC seems to be more involved in maintaining the M-bM-^@M-^\growth signalM-bM-^@M-^] and thus ensure the indeterminate root growth. Total 7 samples (2 replicates of shr-2 mutant (high PHABULOSA expression) vs. 2 replicates of shr-2 phb-6 (low/absent PHABULOSA expression). 3 replicates of Wild type used as reference sample.

2012-12-31 | E-GEOD-33015 | biostudies-arrayexpress

MDA-MB-231 cells: shMUC4 transfected vs. Control SCR

Project description:Identification of MUC4-associated expression of genes by comparing MUC4 knockdown (MDA-MB-231-shMUC4) and control (MDA-MB-231-SCR). Two-condition experiment, MUC4 knockdown cells vs. control. Biological replicates: 2 control, 2 sh-MUC4 transfected, independently grown and harvested. one replicate per array.

2012-12-31 | E-GEOD-40157 | biostudies-arrayexpress

SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions

Project description:Hydrogen peroxide (H2O2) can act as a signaling molecule that influences various aspects of plant growth and development, including stress signaling and cell death. To unravel the molecular mechanisms that regulate the response towards an impact of increased H2O2 levels in plant cells, we focused on the photorespiration-dependent peroxisomal H2O2 production in Arabidopsis thaliana mutants lacking CATALASE2 (CAT2) activity (cat2-2) and screened for second-site mutations that attenuate the Fv'/Fm' decrease and lesion formation linked to the cat2-2 phenotype. A mutation in the transcriptional regulator SHORT-ROOT (SHR) of the GRAS family rescued the cell death phenotype of cat2-2 plants under photorespiration-promoting conditions in a SCR-independent way, and provoked perturbation of photorespiratory metabolites. SHR deficiency boosted ascorbate levels and prevented the oxidation of the glutathione pool in cat2-2 background upon exposure to photorespiratory stress. These results reveal an unanticipated role for SHR as a regulator of cellular redox homeostasis. Unstressed and stressed samples of 4 genotypes (Col-0, cat2, shr and cat2 shr) in triplicate

2016-07-28 | E-GEOD-77017 | biostudies-arrayexpress

Genome-wide identification of SCARECROW (SCR) direct targets using a custom Agilent promoter array

Project description:ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3’UTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed.

2011-11-23 | GSE30104 | GEO

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