Expression analysis of picloram responsive genes preceding cell elongation in Arabidopsis hypocotyls.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE37217 | GEO | 2012/04/13
SECONDARY ACCESSION(S): PRJNA159197
REPOSITORIES: GEO
Similar Datasets
Project description:In this study we profile expression of target genes downstream of auxin signaling in Arabidopsis hypocotyls elongating in response to auxin. The synthetic auxin picloram is used in order to take advantage of the picloram-resistant auxin receptor mutant afb5-5, which fails to elongate in response to picloram. A 4-plex chip was used for analyzing the transcriptome in hypocotyls dissected from wild-type seedlings following a 30min and 2hr picloram or solvent control treatment. Three biological replicate samples were analyzed, each containing roughly 400 hypocotyls. A 12-plex chip was used for analyzing mRNA from hypocotyls dissected from wild-type and afb5-5 (SALK_110643) mutant seedlings following a 2hr picloram or solvent control treatment. Three biological replicates were analyzed, each containing roughly 700 hypocotyls.
2012-04-12 | E-GEOD-37217 | biostudies-arrayexpress
Project description:fapesp-bra-inra-10-01_bioen_hypocotyl - dark hypocotyls tor rnai - Transcriptional comparison between 2 TOR RNAi mutants versus GUS control. - Sowing after 24h imbibition at 4°C in the dark, on MS1/5, no sucrose, 10 mM ethanol, 8 g/l agar, vertical growth with 3h light, 6 days growth in the dark (20°C), hypocotyls were harvested under green light ; cotyledons and root were removed.
2012-10-10 | GSE41404 | GEO
Project description:The aim of the experiment was to identify early gibberellin (GA) responsive genes in the roots of an Arabidopsis GA deficient mutant.The GA deficient mutant used in this study is a transgenic line overexpressing the PcGA2ox1 gene. This mutant has an identical phenotype to ga1-3, but it does not require exogenous GA treatment for germination.Seeds were germinated on 1xMS + 1% (w/v) sucrose plates containing 0.7% gelrite, and grown under continous light. The plates were orientated vertically.After six days growth the plates were treated with or without 5uM GA4 for 0, 30, 60 and 180 minutes.Approximately 400 hypocotyls were harvested per timepoint using a razorblade and after excision the hypocotyls were frozen in liquid nitrogen giving a total of 7 experimental samples (1: untreated, 2: 30 mins GA4, 3: 30 mins untreated, 4: 60 mins GA4, 5: 60 mins untreated, 6: 180 mins GA4, 7: 180 mins untreated. Three biological replicates were performed giving a total of 21 root samples. Total RNA was isolated from the roots using the QIAGEN RNeasy method. Keywords: Expression profiling by array
2009-11-18 | GSE18985 | GEO
Project description:fapesp-bra-inra-10-01_bioen_hypocotyl - dark hypocotyls tor rnai - Transcriptional comparison between 2 TOR RNAi mutants versus GUS control. - Sowing after 24h imbibition at 4M-BM-0C in the dark, on MS1/5, no sucrose, 10 mM ethanol, 8 g/l agar, vertical growth with 3h light, 6 days growth in the dark (20M-BM-0C), hypocotyls were harvested under green light ; cotyledons and root were removed. 4 dye-swap - normal vs rnai mutant comparaison
2012-10-10 | E-GEOD-41404 | biostudies-arrayexpress
Project description:The aim of the experiment was to identify early gibberellin (GA) responsive genes in the roots of an Arabidopsis GA deficient mutant.The GA deficient mutant used in this study is a transgenic line overexpressing the PcGA2ox1 gene. This mutant has an identical phenotype to ga1-3, but it does not require exogenous GA treatment for germination.Seeds were germinated on 1xMS + 1% (w/v) sucrose plates containing 0.7% gelrite, and grown under continous light. The plates were orientated vertically.After six days growth the plates were treated with or without 5uM GA4 for 0, 30, 60 and 180 minutes.Approximately 400 hypocotyls were harvested per timepoint using a razorblade and after excision the hypocotyls were frozen in liquid nitrogen giving a total of 7 experimental samples (1: untreated, 2: 30 mins GA4, 3: 30 mins untreated, 4: 60 mins GA4, 5: 60 mins untreated, 6: 180 mins GA4, 7: 180 mins untreated. Three biological replicates were performed giving a total of 21 root samples. Total RNA was isolated from the roots using the QIAGEN RNeasy method. Keywords: Expression profiling by array 21 samples were used in this experiment
2009-11-17 | E-GEOD-18985 | biostudies-arrayexpress
Project description:Transcriptional profiling of diploid and tetraploid Arabidopsis dark-grown hypocotyls. The aim of this study was to identify ploidy-related genes involved in the determination of cell size. This study showed that a group of genes involved in lipid transport/localization/binding were downregulated in a defined region of the tetraploid hypocotyl when compared to the diploid hypocotyl.
2015-07-16 | GSE69349 | GEO
Project description:MicroRNAs and phytophormes are all small molecular signals that play important roles in regulating development and environmental responses in plants. The interplay between them allow the plants to better converge multiple inner and outer signals to optimizing their survival strategy. So far, the knowledge of how miRNAs are involved in brassinosteroid (BR) signaling is lacking. Here, we report the finding of miR394 and its target gene LEAF CURLING RESPONSENESS (LCR), which were transcriptionally responsive to BR, participate in BR signaling in regulating hypocotyls elongation in Arabidopsis. By phenotypic analyzing of a set of transgenic and mutants, miR394 was found to act as a negative regulator in BR signaling in hypocotyls elongation, while its target gene on the contrary. Genetically, miR394 functions upstream of BIN2 and BZR1/BES1, but partially downstream or independent with BRI1 and BSU1. RNA-seq analysis further supports that miR394 inhibits BR signaling through BIN2 because miR394 co-regulate significant number of genes together with BIN2. Additionally, miR394 improved the accumulation of BIN2 but decreased the protein amount of BZR1 and BES1, which can be phosphorylated by BIN2. miR394 also repressed the transcription of PRE1/5/6 and EXP8, the key hypocotyls elongation regulating genes, which had been reported to be BZR1/BES1 targets. These findings revealed a new pathway that miRNA involved in BR signaling in Arabidopsis.
2019-08-01 | GSE114214 | GEO
Project description:We hypothesized a convergence of transcriptome profiles in hypocotyls of low blue light (LB) or low red/far red light (LRFR) treated seedlings as both conditions trigger hypocotyl cell elongation. To test this hypothesis, we did a transcriptome analysis in of 5d-old long-day (LD)-grown Col-0 (wild type, WT), pif457, and yuc2589 seedlings treated for 3 hours with LB, LRFR or remaining in the same light condition (WL). We used dissected cotyledons and hypocotyls to characterize the LB and LRFR response in both organs and determine their dependency on PIFs and YUC-mediated auxin biosynthesis.
2022-08-08 | GSE174655 | GEO
Project description:pepper Cotyledons and hypocotyls Raw sequence reads
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Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation. Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day
2011-06-19 | E-GEOD-27508 | biostudies-arrayexpress