Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA110659 | ENA |
REPOSITORIES: ENA
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Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Keywords: cell type comparison
2009-04-06 | GSE13596 | GEO
Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Experiment Overall Design: Three replicates were used CLV3p, CLV3n and FILp, while for WUSp only two replicates were used. CLV3n cells lacks CLV3p cell type.
2009-04-11 | E-GEOD-13596 | biostudies-arrayexpress
Project description:Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types. All the cells in a mature plant’s SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex. Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development. To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1. We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations. This gene expression map represents data from 10 different cell types from Arabidopsis SAM. It will be first step in defining the function of many unknown genes in model plant Arabidopsis.
2014-05-15 | GSE28109 | GEO
Project description:Shoot apical meristem (SAM) of higher plant composed of a few distinct cell types. All the cells in a mature plant’s SAM derived from 30~35 stem cells reservoir which are located at the tip of the apex. Plants ability to give rise diverse cell types from a pool of pluripotent stem cells requires orchestrated gene network that controls the cell fate commitment during the meristem development. To understand, how gene regulatory networks control cell identities switches during cell differentiation requires resolution in recording their gene expression pattern at single cell resolution. An earlier expression map involving three-cell population of stem cell niche revealed complex expression pattern among the cell types1. We developed this approach further and report here a gene expression map using cell-sorting methods for fluorescent protein marked cells in Arabidopsis shoot. The map covered 10 cell populations. This gene expression map represents data from 10 different cell types from Arabidopsis SAM. It will be first step in defining the function of many unknown genes in model plant Arabidopsis. Based on the in situ hybridization we identified 7 new cell types specific gene expression patterns. The promoters of these genes were used to generate fluorescent reporters. After treating the SAM with protoplasting cocktail, we sorted the fluorescent protein tagged cells using fluorescent activated cell sorter (FACS). The purified cell population was used to isolate RNA. Two round of RNA amplification was performed before microarray hybridization.
2014-05-15 | E-GEOD-28109 | biostudies-arrayexpress
Project description:The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity.
2011-12-07 | GSE34209 | GEO
Project description:Study on the role of Arabidopsis thaliana RDR1 and other RNAi factors in the exclusion of RNA viruses from the shoot apical meristem stem cells
2023-10-09 | GSE221157 | GEO
Project description:Study on the role of Arabidopsis thaliana RDR1 and other RNAi factors in the exclusion of RNA viruses from the shoot apical meristem stem cells
2023-10-09 | GSE242499 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. Moreover, the homeobox WUSCHEL protein, known to control stem cell pool, has been found to interact with the ARGONAUTE protein, thus mediating NO signaling in the shoot apical meristem (SAM) is crucial for the stem cell fate. Our results reveal an important mechanism that NO is key to stem cell maintenance and differentiation.
2023-12-01 | GSE244737 | GEO
Project description:Despite the importance of Nitric oxide (NO) in both plant and animal development, the regulatory and mechanism of NO function remain elusive. Here, we show that NO promotes Arabidopsis shoot stem cell differentiation via the RNA directed DNA Methylation (RdDM) pathway. Knocking out of the components of the RdDM pathway causes meristematic defects, and at least in part could block the stem cell and niche-specific genes responding to the NO signaling. Moreover, the homeobox WUSCHEL protein, known to control stem cell pool, has been found to interact with the ARGONAUTE protein, thus mediating NO signaling in the shoot apical meristem (SAM) is crucial for the stem cell fate. Our results reveal an important mechanism that NO is key to stem cell maintenance and differentiation.
2023-12-01 | GSE216951 | GEO