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E-GEOD-79856

ABSTRACT: Transcription profiling by high throughput sequencing of estradiol-inducible overexpression of transcription factor WRKY75 in Arabidopsis thaliana

PROVIDER: E-GEOD-79856 | ExpressionAtlas | 2017-02-20

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-79856-analysis-methods.tsv	Tabular
	E-GEOD-79856-analytics.tsv	Tabular
	E-GEOD-79856-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-79856-configuration.xml	Xml
	E-GEOD-79856-g2_g1-mvaPlot.png	Other

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Arabidopsis thaliana

Project description:Transcriptome analysis of estradiol-inducible overexpression of transcription factor WRKY75 in Arabidopsis thaliana

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Transcriptome analysis of estradiol-inducible overexpression of transcription factor WRKY75 in Arabidopsis thaliana

2016-04-03 | GSE79856 | GEO

Transcriptome analysis of estradiol-inducible overexpression of transcription factor WRKY75 in Arabidopsis thaliana

Project description:Sequence-specific transcription factor WRKY75 is highly responsive to reactive oxygen species on transcriptional level in the rosettes of Arabidopsis thaliana. In addition, it acts in developmental responses, acquisition of nutrients, and in stress responses. In the root, WRKY75 is a repressor of root hair formation, it regulates the phosphate starvation response, and the response to certain pathogens. In order to find the target genes of WRKY75, the effects of estradiol-inducible overexpression of WRKY75 on transcriptome was studied using RNA-seq. Two independent inducible WRKY75 overexpressor lines (N2102362 and N2102363) were treated with estradiol for 3 hours and four biological replicates, five plant per replicate, were used for RNA-seq. As a control, wild type Col-0 was treated with estradiol or water for 3 hours and three biological replicates, five plant per replicate, were used for RNA-seq.

2016-04-03 | E-GEOD-79856 | biostudies-arrayexpress

OBP4 modifies root growth, cell elongation and callus formation

Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by overexpressing OBP4 transcription factor under teh control of an estradiol inducible promoter This work analyzes the effect of overexpression the transcription factor OBP4 in gene transcription. Details of how ectopic expression affects root development and callus formation are described in Rammirez-Parra et al. (submitted)

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Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

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Genome wide expression analysis of EST-induced EBE-XVE using Affymetrix ATH1 array

Project description:Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed. In order to identify potential direct/early target genes of EBE transcription factor, estradiol inducible overexpression system was used. Three week old Arabidopsis EBE-XVE (line 14) and WT seedlings were treated with ß-estradiol (2µM) for 45 min. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in 3 biological replications and genes differentially expressed between estradiol treated EBE-XVE and WT plants were identified as potential early targets of EBE.

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The PXC3 receptor-like kinase constitutively interacts with BAK1 and is involved in vascular development in Arabidopsis.

Project description:We designed an experiment to identify BAK1 interactors considering that it could be a coreceptor for the GOLVEN6 (GLV6) signaling peptide involved in lateral root organogenesis in Arabidopsis thaliana. A BAK1pro:BAK1-GFP/bak1-4 line crossed to an estradiol-inducible GLV6 overexpression line (BAK1pro:BAK1-GFP/bak1-4xiGLV6) was treated with mock or estradiol followed by affinity purification mass spectrometry (AP-MS) experiments using anti-GFP beads in microsomal-enriched fractions. Statistical analysis of estradiol-treated vs. mock seedlings did not reveal significant differences. Nevertheless, we remarked that regardless of the treatment, several LRR-RLKs co-eluted with BAK1-GFP, comprising known, as well as, unknown interactors. We confirmed interaction of BAK1 with these LRR-RLKs by BIFC and identified the PXC3 receptor as a BAK1 constitutive interactor, which was further verified by co-IP.

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RNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana

Project description:The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for the GLV6 peptide) backgrounds, in combination with gravistimulation induced lateral root formation, the RGI receptor dependent transcriptional effects of GLV6 overexpression were characterized. An estradiol inducible GLV6 overexpression line in a wildtype (iGLV6) and in an rgi1rgi5 double receptor mutant background (rgi1rgi5/iGLV6) were used. 4-day old seedlings of both lines were gravistimulated (vertically grown seedlings were turned counterclockwise by 90°) to induce lateral root initiation in the resulting root bends. 8h after gravistimulation, seedlings of both lines were treated with 2µM of estradiol to induce GLV6 overexpression, or DMSO as a mock treatment. 3h and 6h after treatment, root bends were dissected and collected for RNA-sequencing. This yielded a total of 8 samples per replicate; 3h mock treated iGLV6 (IM3), 3h estradiol treated iGLV6 (IE3), 3h mock treated rgi1rgi5/iGLV6 (RM3), 3h estradiol treated rgi1rgi5/iGLV6 (RE3), 6h mock treated iGLV6 (IM6), 6h estradiol treated iGLV6 (IE6), 6h mock treated rgi1rgi5/iGLV6 (RM6), 6h estradiol treated rgi1rgi5/iGLV6 (RE6). For each sample, 4 replicates were obtained. This setup enabled the comparison of the GLV6 induced transcriptional effects between wildtype and rgi1rgi5 mutants at 2 time points after treatment, in samples that are strongly enriched for lateral root initiation events.

2022-02-13 | E-MTAB-10891 | biostudies-arrayexpress

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