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Auxin mediated gene expression in WT, arf7, arf19 and arf7 arf19 mutants

ABSTRACT: RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5ÂµM IAA) for 2 h. Lines used for this study: Columbia wild-type nph4-1(arf7) single mutant arf19-1 single mutant nph4-1 arf19-1 double mutant Treatment: Control (EtOH) Auxin treated (5ÂµM IAA) Keywords = Auxin Keywords = Auxin response factor Keywords: parallel sample

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Athanasios Theologis

PROVIDER: E-GEOD-627 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.

Okushima Yoko Y Overvoorde Paul J PJ Arima Kazunari K Alonso Jose M JM Chan April A Chang Charlie C Ecker Joseph R JR Hughes Beth B Lui Amy A Nguyen Diana D Onodera Courtney C Quach Hong H Smith Alison A Yu Guixia G Theologis Athanasios A

The Plant cell 20050119 2

The AUXIN RESPONSE FACTOR (ARF) gene family products, together with the AUXIN/INDOLE-3-ACETIC ACID proteins, regulate auxin-mediated transcriptional activation/repression. The biological function(s) of most ARFs is poorly understood. Here, we report the identification and characterization of T-DNA insertion lines for 18 of the 23 ARF gene family members in Arabidopsis thaliana. Most of the lines fail to show an obvious growth phenotype except of the previously identified arf2/hss, arf3/ett, arf5 ...[more]

PMID: 15659631

Similar Datasets

Auxin mediated gene expression in WT, arf7, arf19 and arf7 arf19 mutants

Project description:RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Lines used for this study: Columbia wild-type nph4-1(arf7) single mutant arf19-1 single mutant nph4-1 arf19-1 double mutant Treatment: Control (EtOH) Auxin treated (5µM IAA) Keywords = Auxin Keywords = Auxin response factor Keywords: parallel sample

2005-10-19 | GSE627 | GEO

Transcription profiling of Arabidopsis seedlings treated with auxin vs. controls

Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5ÂµM IAA) for 2 h.

2008-06-14 | E-GEOD-630 | biostudies-arrayexpress

Auxin-mediated gene expression in WT, iaa17, axr3 and iaa5iaa6iaa19 mutants

Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5�M IAA) for 2 h. Columbia (WT), IAA17 loss of function mutant allele (iaa17-2), IAA17 gain of function mutant allele (axr3-1) and iaa5 iaa6 iaa19 triple loss of function mutant allele (i5i6i19) were used for this study. Each experimental condition has three true replicates for a total of 24 hybridizations. Data Keywords: parallel sample

2005-12-01 | GSE629 | GEO

Transcription profiling of Arabidopsis auxin mediated gene expression in wild type and arf2-6 mutant

Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5ÂµM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis:; Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The âRâ environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis.

2008-06-14 | E-GEOD-631 | biostudies-arrayexpress

Auxin mediated gene expression in WT and arf2-6 mutant

Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis: Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The “R” environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis. Keywords = Auxin Keywords = Auxin response factor Keywords: other

2005-10-19 | GSE631 | GEO

Transcriptomic analysis of Col and arf7 responding to auxin

Project description:The goal of this study is to clarify the function of ARF7 in the pathway of auxin inducing lateral root development. We isolated total RNA from the roots of 8-day-old Col-0 and arf7 seedlings. New genes act downstream of ARF7 after responding to auxin treatment, during the lateral root formation, are discovered.

2018-11-10 | GSE122355 | GEO

Transcriptomic analysis of Col and arf7 responding to auxin in hypocotyl

Project description:The goal of this study is to clarify the function of ARF7 in the pathway of auxin inducing the process responding to gravity in hypocotyl. We isolated total RNA from the hypocotyls of 4-day-old Col-0 and arf7 seedlings that were grown in the darkness. New genes act downstream of ARF7 after responding to auxin treatment, responding to gravity, are discovered.

2019-08-30 | GSE136635 | GEO

Natural variation of auxin response

Project description:To assess natural variation of downstream auxin responses we subjected 7 different arabidopsis ecotypes to a time course of auxin treatments. 7d-old seedlings grown in liquid culture have been treated for 0, 30 min, 1h and 3h with 1 µM IAA. Keywords: Expression profilling by array

2009-11-18 | GSE18975 | GEO

BiAux modulates auxin co-receptors activity to form lateral roots

Project description:The root system plays an essential role in plant growth and adaptation to the surrounding environment. Lateral roots (LR) originate postembryonically from a group of pericycle founder cells (FC) that are specified by a root clock in an auxin dependent manner and extend the root´s surface. Auxin perception entails the physical interaction of TIR1 or AFBs proteins with Aux/IAA repressors to form a co-receptor system. Despite the apparent simplicity, how a specific TIR1/AFBs - Aux/IAA module is assembled is not completely understood. Here, we have identified and characterized a novel natural compound, called BiAux, that is a N-glucoside bisindole conjugate. This compound or rBiAux, an improved reduced form, precisely promote FC specification and lateral root emergence without affecting other auxin-related responses, including root growth. Genetic analyses demonstrated that rBiAux signaling requires the function of TIR1 and AFB2 receptors. Remarkable, rBiAux enhances TIR1 or AFB2 interaction with Aux/IAA28 and Aux/IAA18, two regulators of FCs and lateral root formation. Furthermore, rBiAux signaling seems to be dependent on ARF7, a transcription factor involved in FC specification and LR formation. Taken together, our data indicate that BiAux enhances the activity of auxin co-receptors involved in FC specification and lateral root formation.

2024-06-05 | GSE234606 | GEO

SLR/IAA14-dependent auxin induced lateral root initiation

Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Keywords: time-course wild type vs mutant comparison

2005-11-01 | GSE3350 | GEO

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