Ontology highlight
ABSTRACT:
PROVIDER: PRJNA678414 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13060600_1.fastq.gz | Fastqsanger.gz | |||
| SRR13060600_2.fastq.gz | Fastqsanger.gz | |||
| SRR13060601_1.fastq.gz | Fastqsanger.gz | |||
| SRR13060601_2.fastq.gz | Fastqsanger.gz | |||
| SRR13060602_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 4 of the supplementary material of the reference article has been reproduced here. In this model, the fluctuations of auxin level is represented using sinux function. Time evolution of the variables AUX/IAA (I) and mRNA (R) are plotted, under the influence of fluctuations of auxin level. pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000352 | BioModels
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoo
t apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D
, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M
, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development.
It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is
sensed in space and time. The control of gene expression in response to auxin involves a complex netwo
rk of over 50 potentially interacting transcriptional activators and repressors, the auxin response fac
tors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the sho
ot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive ex
pression map and full interactome uncovered an unexpectedly simple distribution and structure of this p
athway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering
capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predic
tions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunct
ion with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin
signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 3 of the supplementary material of the reference article has been reproduced here. Time evolution of all the variables in the model are plotted, under the influence of a step input of auxin level (auxin=5, when time>1000; 0.11, otherwise). pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000351 | BioModels
Project description:Rapamycin-sensitive transgenic Arabidopsis lines (BP12) expressing yeast FK506 Binding Protein12 (FKBP12) were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf and shoot growth and development leading to poor nutrient uptake and light energy utilization. Genetic and physiological studies together with RNA-Seq and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and lifespan in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, ribosomal RNA and protein synthesis.
2012-12-18 | GSE42968 | GEO
Project description:Gene expression in the shoot apex of 3-week old Arabidopsis thaliana (ecotype Col-0) was compared to DRB2 (AT2G28380) null mutants.
2014-07-01 | E-MTAB-2586 | biostudies-arrayexpress
Project description:We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem. We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem. Populus tomentosa shoot apex and mature xylem were taken for RNA extraction and hybridization on Affymetrix microarrays.CB2009304-C and CB2009304-D from shoot apex, CB2009304-G and CB2009304-H from mature xylem.
2013-04-23 | E-GEOD-46312 | biostudies-arrayexpress
Project description:We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem. We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem.
2013-04-23 | GSE46312 | GEO
Project description:Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, and alterations to this interplay in Arabidopsis thaliana produce defects in leaf polarity and shoot apical meristem (SAM) organisation. Although the miR394-LCR node has been documented in Arabidopsis, the identification of proteins targeted by LCR F-box itself has proven problematic. Here, a proteomic analysis of shoot apices from plants with altered LCR levels identified a member of the Major Latex Protein (MLP) family gene as a potential LCR F-box target. Bioinformatic and molecular analyses also suggested that other MLP family members are likely to be targets for this post-translational regulation. Direct interaction between LCR F-Box and MLP423 was validated. Additional MLP members had reduction in protein accumulation, in varying degrees, mediated by LCR F-Box. Transgenic Arabidopsis lines, in which MLP28 expression was reduced through an artificial miRNA technology, displayed severe developmental defects, including changes in leaf patterning and morphology, shoot apex defects, and eventual premature death. These phenotypic characteristics resemble those of Arabidopsis plants modified to over-express LCR. Taken together, the results demonstrate that MLPs are driven to degradation by LCR, and indicate that MLP gene family is target of miR394-LCR regulatory node, representing potential targets for directly post-translational regulation mediated by LCR F-Box. In addition, MLP28 family member is associated with the LCR regulation that is critical for normal Arabidopsis development.
2016-07-19 | PXD002390 | Pride