Dataset Information

Single cell RNA-seq data of Arabidopsis roots

ABSTRACT: Single cell RNA-seq data of Arabidopsis roots

PROVIDER: PRJNA1093461 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28503600.fastq.gz	Fastqsanger.gz
	SRR28503601.fastq.gz	Fastqsanger.gz
	SRR28503602.fastq.gz	Fastqsanger.gz
	SRR28503603.fastq.gz	Fastqsanger.gz
	SRR28503604.fastq.gz	Fastqsanger.gz

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Project description:Muraro2014 - Vascular patterning in Arabidopsis roots Using a multicellular model, maintanence of vascular patterning in Arabidopsis roots has been studied. The model that is provided here is the single-cell version of the model. The two-cell and multicellular models described in the paper can be downloaded as python scripts (follow the curation tab to get these files). This model is described in the article: Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Muraro D, Mellor N, Pound MP, Help H, Lucas M, Chopard J, Byrne HM, Godin C, Hodgman TC, King JR, Pridmore TP, Helariutta Y, Bennett MJ, Bishopp A. Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):857-62. Abstract: As multicellular organisms grow, positional information is continually needed to regulate the pattern in which cells are arranged. In the Arabidopsis root, most cell types are organized in a radially symmetric pattern; however, a symmetry-breaking event generates bisymmetric auxin and cytokinin signaling domains in the stele. Bidirectional cross-talk between the stele and the surrounding tissues involving a mobile transcription factor, SHORT ROOT (SHR), and mobile microRNA species also determines vascular pattern, but it is currently unclear how these signals integrate. We use a multicellular model to determine a minimal set of components necessary for maintaining a stable vascular pattern. Simulations perturbing the signaling network show that, in addition to the mutually inhibitory interaction between auxin and cytokinin, signaling through SHR, microRNA165/6, and PHABULOSA is required to maintain a stable bisymmetric pattern. We have verified this prediction by observing loss of bisymmetry in shr mutants. The model reveals the importance of several features of the network, namely the mutual degradation of microRNA165/6 and PHABULOSA and the existence of an additional negative regulator of cytokinin signaling. These components form a plausible mechanism capable of patterning vascular tissues in the absence of positional inputs provided by the transport of hormones from the shoot. This model is hosted on BioModels Database and identified by: BIOMD0000000522 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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Single cell RNA-seq data of Arabidopsis roots

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