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Genome wide identification of ORE1 early target genes

ABSTRACT: Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE37536 | GEO | 2013/01/01

SECONDARY ACCESSION(S): PRJNA163857

REPOSITORIES: GEO

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Genome wide identification of ORE1 early target genes

Project description:Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts To identify genes more rapidly responding to elevated ORE1 expression we here repeated the previous experiment (Balazadeh et al., 2010), but shortened the EST induction time to 2 h (ORE1-IOE-2h dataset). Furthermore, to exclude potential misinterpretation due to EST treatment we also included an experiment where we transiently expressed a 35S::ORE1 construct in Arabidopsis mesophyll cell protoplasts and extracted RNA 6 h after the transfection (35S::ORE1-6h dataset);

2013-01-01 | E-GEOD-37536 | biostudies-arrayexpress

Genome-wide identification of RD26 target genes

Project description:Global transcriptome patterns were determined in 2-week-old RD26-IOE seedlings after 2h (one biological replicate) or 5h (two biological replicates) estradiol (EST) or ethanol (mock) treatment. EST-induced expression of RD26.

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Genome wide identification of SHYG early target genes

Project description:Global transcriptome patterns were performed using SHYG-IOE-5h (5h after Estradiol and Mock treatment)

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Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

2014-08-30 | GSE54676 | GEO

Genome wide identification of SHYG early target genes

Project description:Global transcriptome patterns were performed using SHYG-IOE-5h (5h after Estradiol and Mock treatment) To identify genes more rapidly responding to elevated SHYG , we perfromed gene expression profiling (Affymetrix) upon 5h Est treatment of SHYG-IOE plants.

2013-12-29 | E-GEOD-38721 | biostudies-arrayexpress

Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells

2007-08-17 | GSE8248 | GEO

Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

Project description:Global transcriptome patterns were obtained from ATAF1-IOE seedlings at 1 h, 2 h and 5 h after estradiol induction or mock treatment, and from mature ATAF1-IOE leaves at 5 h after estradiol induction or mock treatment. To identify genes rapidly responding to elevated ATAF1 expression estradiol induction experiments were performed on ATAF1-IOE seedlings after 1 h, 2 h and 5 h of ATAF1 induction. In addition, expression profiles were obtained from mature leaves after 5 h of ATAF1 induction.

2014-08-30 | E-GEOD-54676 | biostudies-arrayexpress

Transcription profiling of Arabidopsis mesophyll cells to identify KIN10-target genes

Project description:The goal of this experiment was to explore the extent of KIN10 (At3g01090) transcriptional regulation and identify its early target genes in Arabidopsis mesophyll protoplasts. Results suggest that KIN10 targets a remarkably broad array of genes that orchestrate transcription networks, promote catabolism and autophagy, and suppress anabolism and ribosome biogenesis. The transient expression condition ruled out secondary or long-term effects of metabolism and growth, and circumvented experimental limitations caused by redundancy and embryonic lethality observed in mammals and plants. Experiment Overall Design: Analysis of the transcript changes induced by transient KIN10 (At3g01090) expression (6h) in Arabidopsis mesophyll protoplasts using protoplasts similarly transfected with control plasmid DNA for comparison. To maximize the significance of the duplicated experimental data for defining differentially expressed genes, the biologically independent experiments were carefully performed by two individuals using different soil, plants, growth chambers, DNAs and microarray facilities for hybridization and scanning to cover potential technical and biological variations. For each pair (control & KIN10) of large-scale protoplast transfection experiments, about 3 million protoplasts were isolated from the fifth and sixth leaves of 36 randomly picked plants and pooled. Experiment Overall Design: RNA samples isolated from control and KIN10-transfected protoplasts were subjected to quality controls, including RNA quality and quantity inspection by gel electrophoresis and staining as well as consistent gene expression changes by duplicated real-time quantitative RT-PCR analyses of selected marker genes.

2008-06-16 | E-GEOD-8257 | biostudies-arrayexpress

Transcription profiling of Arabidopsis mesophyll cells to identify hypoxia-inducible genes

Project description:The goal of this experiment was to investigate the early transcript changes (6h) induced by hypoxia treatment in mesophyll protoplasts. A single pair (control & hypoxia) of GeneChipsÂ® was used to confirm that hypoxia treatment altered the expression of an overlapping set of genes controlled by KIN10 (At3g01090) in Arabidopsis mesophyll protoplasts. Experiment Overall Design: For the hypoxic treatment protoplasts were submerged in mannitol buffer and the hypoxia condition was confirmed by the activation of the well-established early marker genes ADH (alcohol dehydrogenase, At1g77120) and PDC1 (pyruvate decarboxylase-1, At4g33070) based on RT-PCR and GeneChipÂ® analyses. Results show a clear overlap in genes induced under hypoxic conditions and those induced by KIN10 expression in protoplasts. The overlap of the gene expression profiles was confirmed by triplicated real-time quantitative RT-PCR analyses of selected marker genes.

2008-06-16 | E-GEOD-8248 | biostudies-arrayexpress

Identification of CPK5ac and CPK11ac early target genes in Arabidopsis mesophyll cells

Project description:The goal of this experiment was to identify the early target genes of constitutively activated CPK5ac and CPK11ac in Arabidopsis mesophyll cells that are involved in early flagellin responses important for plant innate immunity. We used the microarrays to detail the global program of gene expression underlying initial calcium responses to microbial associated molecualr patterns (MAMPs). Arabidopsis mesophyll protoplasts were transfected with plasmid DNA to express constitutively active CPK5ac or CPK11ac for 6 hr. Transcript profiles were analyzed and compared between cells transfected with control DNA and CPK5ac or CPK11ac DNA to identify early CPK5ac and CPK11ac target genes.

2010-03-18 | E-GEOD-16471 | biostudies-arrayexpress

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