Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA139823 | 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: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:Cell type-specific auxin responses in the Arabidopsis thaliana root
| PRJNA152235 | ENA
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Cell type-specific expression atlas of the early Arabidopsis thaliana embryo
| PRJNA350282 | ENA
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. 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:How bacteria from the microbiota modulate the physiology of its host is an important question to address. Previous work revealed that the metabolic status of Arabidopsis thaliana was crucial for the specific recruitment of Streptomycetaceae into the microbiota. Here, the Arabidopsis-Actinacidiphila interaction was further depicted by inoculating axenic Arabidopsis with Actinacidiphila cocklensis DSM 42063 or Actinacidiphila bryophytorum DSM 42138(previously named Streptomyces cocklensis and Streptomyces bryophytorum). We demonstrated that these two bacteria colonize A. thaliana wild-type plants, but their colonization efficiency was reduced in a chs5 mutant with defect in isoprenoid, phenylpropanoids and lipids synthesis. We observed that those bacteria affect the growth of the chs5 mutant but not of the wild-type plants. Using a mass spectrometry-based proteomic approach, we showed a modulation of the Arabidopsis proteome and in particular its components involved in photosynthesis or phytohormone homeostasis or perception by A. cocklensis and A. bryophytorum. This study unveils specific aspects of the Actinacidiphila-Arabidopsis interaction, which implies molecular processes impaired in the chs5 mutant and otherwise at play in the wild-type. More generally, this study highlights complex and distinct molecular interactions between Arabidopsis thaliana and bacteria belonging to the Actinacidiphila genus.
2024-01-29 | PXD041221 | Pride
Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche
| PRJNA110659 | ENA
Project description:The aim of this project is to deeply map the proteome of mitochondria from the model plant Arabidopsis thaliana. For this purpose, mitochondria were isolated from Arabidopsis cell cultures, their proteins extracted and processed using SP3 digestion. To achieve high sequence coverage, the proteins were digested with a total of six different proteases and measured using sensitive timsTOF Pro hardware and TIMS fractionation.
2023-08-02 | MSV000092578 | MassIVE