Whole-body integration of gene expression and single-cell morphology
| Autor: | Emily L. Savage, Oleg Simakov, Anna Kreshuk, Pedro Machado, Christian Tischer, Valentyna Zinchenko, Kimberly Meechan, Yannick Schwab, Rainer W. Friedrich, Paola Bertucci, Benjamin Titze, Detlev Arendt, Rachel M. Templin, Christel Genoud, Hernando Martínez Vergara, Constantin Pape, Adrian A. Wanner |
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| Rok vydání: | 2020 |
| Předmět: |
0303 health sciences
Cell type Effector Cell Computational biology Biology Cell morphology 03 medical and health sciences 0302 clinical medicine medicine.anatomical_structure Cytoarchitecture Gene expression medicine 14. Life underwater Gene Transcription factor 030217 neurology & neurosurgery 030304 developmental biology |
| Zdroj: | bioRxiv Cell |
| DOI: | 10.1101/2020.02.26.961037 |
| Popis: | SummaryAnimal bodies are composed of hundreds of cell types that differ in location, morphology, cytoarchitecture, and physiology. This is reflected by cell type-specific transcription factors and downstream effector genes implementing functional specialisation. Here, we establish and explore the link between cell type-specific gene expression and subcellular morphology for the entire body of the marine annelidPlatynereis dumerilii. For this, we registered a whole-body cellular expression atlas to a high-resolution electron microscopy dataset, automatically segmented all cell somata and nuclei, and clustered the cells according to gene expression or morphological parameters. We show that collective gene expression most efficiently identifies spatially coherent groups of cells that match anatomical boundaries, which indicates that combinations of regionally expressed transcription factors specify tissue identity. We provide an integrated browser as a Fiji plugin to readily explore, analyse and visualise multimodal datasets with remote on-demand access to all available datasets. |
| Databáze: | OpenAIRE |
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