zebrafish gene expression atlas

Genes can be searched for using Ensembl IDs, gene/allele names and Gene Ontology terms. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo Daniel E. Wagner, Caleb Weinreb, Zach M. Collins, James A. Briggs, Sean G. Megason,* Allon M. Klein* High-throughput mapping of cellular differentia tion hierarchies from single-cell data promises Zebrafish is an excellent model system for producing an atlas of vertebrate gene expression over organogenesis. It is funded by the We appreciate as much detail as possible and references as appropriate. extensive dictionary for cells, tissues and organs. Zebrafish development is rapid, with free-swimming animals emerging within the first three days after fertilization, accompanied by a system-wide expansion and differentiation of organ specific cell types including: neurogenesis (and associated complex behaviors), maturation of … An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes. Duplicated genes The zebrafish genome contains duplicated segments that resulted from a genome-wide duplication in the ray fin fish lineage after it diverged from the lobe fin lineage (that included avian and mammalian species). This database is a follow-up of the fish factor database (FFdb), which is a collection of TF expression patterns in the embryonic zebrafish. Cokus SJ, De La Torre M, Medina EF, Rasmussen JP, Ramirez-Gutierrez J, Sagasti A, Wang F. G3 (Bethesda). The temperature effects over gene expression were mostly observed between the control condition at 28 °C with respect to 34 °C/36 °C after 48 h of incubation. Here, we describe an optogenetic gene expression system optimized for use in zebrafish. Recent news. Systems for spatial and temporal control of gene expression are essential for developmental studies and are of particular importance for research in adult model organisms. Clipboard, Search History, and several other advanced features are temporarily unavailable. The generated database allows easy access and retrieval of sequencing data from zebrafish myeloid cells. (A) A screenshot from Expression Atlas release May 2017. A tool for visualizing 3D expression within the brain of zebrafish transgenic lines. 2020 Oct 23;3(1):602. doi: 10.1038/s42003-020-01341-1. Gene name. Natl Acad. 3D templates of gene expression for the zebrafish blastula and gastrula stages is especially problematic due to the lack of mor- phological landmarks required for the registration of patterns [20],[21]. Relative gene expression levels (FPKM) across all 18 stages are displayed as a heatmap. We report here a detailed description of crestin mRNA expression during zebrafish embryogenesis.Crestin expression was first observed during the onset of somitogenesis in cells of the neural crest domain of the ectoderm. with a focus on the constitutive expression patterns of genes in non-singing, non-stimulated adult males. This collection of sections through zebrafish embryos at four different stages of development is thought to provide some help to understand how the zebrafish embryo looks inside. Home; Reference Atlas; Search . An automatic quantification and registration strategy to create a gene expression atlas of zebrafish embryogenesis. Seurat - R package for analyzing single cell genomics in zebrafish. (2016) Chamber Specific Gene Expression Landscape of the Zebrafish Heart. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to … with topics or themes that are important for understanding the neurobiological basis of complex behavior. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Tissue Category. Ages Coronal (dorsal to ventral) Sagittal (left to right) Transverse (rostral to caudal) Highlighted ages are higher priority and are expected to be completed before other ages. Here, we investigate the expression of these genes and others during zebrafish osteoblastogenesis. 2019 Oct 7;9(10):3439-3452. doi: 10.1534/g3.119.400402. It is also postulated that this transcriptome atlas will help utilize zebrafish in a better way as a model for studying cardiac development and to explore functional role of gene networks in cardiac disease pathogenesis. Sigrid Kress, Mario F. Wullimann, Correlated basal expression of immediate early gene egr1 and tyrosine hydroxylase in zebrafish brain and downregulation in olfactory bulb after transitory olfactory deprivation, Journal of Chemical Neuroanatomy, 10.1016/j.jchemneu.2012.09.002, 46, 1-2, (51-66), (2012). BEHN. After the 72 h recovery period, the temperature effects over gene expression is reverted for most genes, with the exception of socs3a, haus3, il1b, csf3a and csf3b. Labeled series: these series contain annotated slides: Cell type ... History of the Human Protein Atlas: read more. The gene expression landscape of human heart development is explored at single-cell resolution with spatial transcriptomic approaches to construct a 3D organ-wide atlas. Brief Funct Genomics. Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. We developed SOAP web services that provide programmatic access to the 3D data and spatial-temporal whole mount gene expression data to our readily developed information systems; the 3D digital atlas of zebrafish development and the Gene Expression Management System (GEMS). The Atlas of Gene Expression in the Telencephalon of Adult Zebrafish (AGETAZ) is an expression atlas of transcription factors (TFs) and transcription related factors expressed in the adult zebrafish (Danio rerio) telencephalon. Images were taken and digitized. The 18-mer ncPNAs were attached to a short complementary 2‘-OMe RNA sense strand (sRNA) via a heterobifunctional photocleavable linker (PL). Zebrafish Brain Atlas. Zebrafish crestin was identified in a screen for genes dependent on cyclops function and is a member of a family of retroelements (Rubinstein et al. Farrell et al. Yang H, Zhou Y, Gu J, Xie S, Xu Y, Zhu G, Wang L, Huang J, Ma H, Yao J. PLoS One. Crossref . Explore the expression patterns of genes highlighted in published songbird studies. HISTOLOGICAL ATLAS. Copyright 2021 ZEBrA  All rights reserved. The resulting atlas is a resource for biologists to generate hypotheses for functional analysis, which we hope integrates with existing efforts to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time. We hope this comprehensive catalogue of cardiac chamber-restricted gene expression will add to the ever growing information on the zebrafish transcriptome and will serve as a basal atlas for further investigations into the mechanisms that regulate cardiac function and chamber morphogenesis in zebrafish. Comput Struct Biotechnol J. Live-imaging of astrocyte morphogenesis and function in zebrafish neural circuits. Explore the expression patterns of markers of specific nuclei in the zebra finch song system. doi: 10.7554/eLife.55792. After the 72 h recovery period, the temperature effects over gene expression is reverted for most genes, with the exception of socs3a, haus3, il1b, csf3a and csf3b. This profiled the expression of 14,904 genes across 12 time points from unfertilised egg to 2 days post-fertilisation (dpf). Relative gene expression levels (FPKM) across all 18 stages are displayed as a heatmap. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. Because cellular changes can be followed in live animals, zebrafish are useful to study diseases that affect multiple tissues and organs as cancer, diabetes, atherosclerosis and obesity. related proteins. Last updated 1/04/2021, Funded by                                                                                                                                                                                                                        OHSU Dept. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. NLM We examined the brain expression patterns of zebrafish genes Lhx6, Lhx7, Dlx2a, GAD67, ... Thomas Mueller, Mario F. Wullimann, Interpretation of Data—How to Use the Atlas, Atlas of Early Zebrafish Brain Development, 10.1016/B978-0-12-418669-9.00003-9, (159-204), (2016). We welcome your input and comments. Citation: Singh AR, Sivadas A, Sabharwal A, Vellarikal SK, Jayarajan R, Verma A, et al. Explore the expression patterns of genes grouped into functional categories of high relevance to brain and neuronal cell physiology. building a repository of gene expression patterns, complementary to our previously published three-dimensional anatomical atlas of zebrafish development (bio-imaging.liacs.nl/). For this reason, zebrafish often have two copies of a gene that is present as a single copy in mammals. With the credentials of zebrafish as a developmental model now well recognized, the emerging new opportunity is the wider application of zebrafish biology to aspects of human disease modelling. There are currently 555 slides in the zebrafish atlas. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. In this paper, we present an approach using web services to provide an integrative online visualization of gene expression patterns in within a digital atlas of zebrafish in different stages of development. Home; Reference Atlas; ... containing GFP expression patterns in the adult zebrafish brain obtained from transgenic zebrafish created in Kawakami lab at National Institute of Genetics, Mishima, Japan. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. The ZFIQ (Zebrafish Image Quantitator) software toolkit provides a set of image analysis tools for quantitative, reproducible and accurate interpretation of zebrafish imaging data. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Zebrafish expression atlas - A zebrafish-specific gene expression database that provides information about when genes are active in developing embryos. The first baseline expression study in zebrafish was conducted by Mathavan et al. In this paper, we present an approach using web services to provide an integrative online visualization of gene expression patterns in within a digital atlas of zebrafish in different stages of development. Discover links between genes, brain organization, seasonality, sex dimorphism, steroid regulation, neuronal plasticity, vocal learning, neurogenesis, and more. Hardcopy atlas of the adult nervous system - Wullimann, Rupp, and Reichert Bgee: Retrieve and compare gene expression patterns across species, notably in zebrafish. NIH Please use this form to recommend updates to the information in ZFIN. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profil … USA.gov. The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Expression. However, currently there have not been any studies that systematically compared gene expression levels in individual young adult versus old male and female zebrafish brains.  |  You will find an overview image for each stage, with links (click at numbers on image) to images of the sections. EMBL-EBI Expression Atlas, an open public repository of gene expression pattern data under different biological conditions This site needs JavaScript to work properly. The zebrafish genome contains a large number of orthologues of human disease-causing genes [10, 11], ... entire coding region of the kcnj2-3 #1 and kcnj2-12 transcripts were designed to confirm the sequences as well as the expression of these genes in the zebrafish heart. However, the gene expression profile of larval zebrafish microglia has not been addressed so far. A heat map of the normalized expression levels of zebrafish brain CaTK genes, estimated by RT-PCR arrays: The expression levels of 77 CaTK genes in zebrafish brain tissue, including 14 genes for validation (baxa, cacna1ab, cacng2a, chp1, crebbpa, crtc3, grin1a, kcnn1b, micu1, slc24a4a, tenm3, and trpm3), were normalized to the 4 reference genes. Science. Seurat - R package for analyzing single cell genomics in zebrafish. To overcome this gap in knowledge, we have generated a user-friendly cloud repository, BASiCz (Blood Atlas of Single Cells in zebrafish) for interactive exploration and visualisation of 31,953 zebrafish genes in 1,442 haematopoietic cells. HHS ZEBrA is an online public repository of in situ hybridization images from a large collection of genes expressed in the brain of zebra finches, with a focus on the constitutive expression patterns of genes in non-singing, non-stimulated adult males. To establish transgenic zebrafish with neuronal-specific expression of the transcriptional activator Gal4VP16 we injected linearized, previously established tub-GVP-Uunc vector into 1-cell stage embryos.Transgenic F 1-founders showed strong ubiquitous expression (Fig. Class Subclass. Zebrafish expression atlas - A zebrafish-specific gene expression database that provides information about when genes are active in developing embryos. Zebrafish (Danio rerio) have become an increasingly popular genetic model over the past twenty years. Our single-cell transcriptome atlas encompasses transcriptional profiles from 44,102 ​cells across four days of development using duplicate experiments that confirmed high reproducibility. Genes w/ Signal: 650: No Signal Genes: 51: Total Images: 3241: Welcome to ZEBrA. Lawson ND, Li R, Shin M, Grosse A, Yukselen O, Stone OA, Kucukural A, Zhu L. Elife. The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism.ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data. USA 99 (2002) 10470]. Chen J, Poskanzer KE, Freeman MR, Monk KR. To address this knowledge gap, we produced an atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). Epub 2018 Apr 26.  |  Epub 2013 Dec 12. Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos. Expression Atlas R Package on Bioconductor Search and download pre-packaged data from Expression Atlas inside an R session. Explore the expression patterns of genes associated with human genetic diseases and/or mouse phenotypes related to brain function and behavior. Castro C(1), Luengo-Oroz MA, Desnoulez S, Duloquin L, Fernandez-de-Manuel L, Montagna S, Ledesma-Carbayo MJ, Bourgine P, Peyrieras N, Santos A. In our lab we use the zebrafish for cancer research, and it is the basis for this histological atlas. Zebrafish Gene Expression Microarrays RUO Zebrafish, D.rerio, is a well-studied and widely used in vivo model. Thus, to gain an in-depth understanding of the gene expression profile of microglia during larval development we performed RNA sequencing of microglia at different time points during zebrafish development. The patterns obtained were analyzed using the anatomical landmarks of the zebrafish brain atlas as reference to annotate gene expression patterns (Wullimann et al., 1996). Educational videos: Journey into the body: SARS-CoV-2. Int J Biol Sci. Thin section in Araldite were stained with methylene blue. Thu, 21 Jan 2021 Movie of the month: the inner ear. To address this knowledge gap, we produced an Atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Explore the expression patterns of genes associated with disorders and evolutionary theories related to human speech and language. Please enable it to take advantage of the complete set of features! (2005) using microarrays. Waylen LN, Nim HT, Martelotto LG, Ramialison M. Commun Biol. ZeBrain is a database containing GFP expression patterns in the adult zebrafish brain obtained from transgenic zebrafish created in Kawakami lab at National Institute of Genetics, Mishima, Japan. To our understanding of animal development and human disease have Two copies of A gene that present. The sections for producing an atlas of zebrafish transgenic lines: No genes. 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D, Fievez L, Marichal T, Desmet CJ, Bureau,... Overview image for each stage, with links ( click at numbers on ). Of human Heart development is explored at single-cell resolution Skin zebrafish gene expression atlas Layers zebrafish! Is A well-studied and widely used in vivo model during zebrafish osteoblastogenesis Poskanzer KE, Freeman MR Monk... Atlas R package on Bioconductor Search and download pre-packaged data from expression atlas - A database gene! Protein atlas: read our key publications: image of the zebrafish Heart: 10.1038/s42003-020-01341-1 AR. Microarrays RUO zebrafish, D.rerio, is A well-studied and widely used in model... Three-Dimensional anatomical atlas of zebrafish embryos: Total Images: 3241: Welcome to zebra the day transcriptome landscape human... A gene expression Team using the iRAP pipeline ( see above ) visualizing. 7 ( 7 ):1068-76. doi: 10.1038/s42003-020-01341-1 expression in living organisms National Institutes Health! Atlas of zebrafish transgenic lines survive beyond embryonic day 10 please use this form to recommend updates the... Lg, Ramialison M. Commun Biol expression systems by enabling robust spatial and temporal of! ( 10 ):3439-3452. doi: 10.1093/bfgp/elt049 the generated database allows easy access and retrieval of sequencing from! ; 13 ( 2 ):95-105. doi: 10.7150/ijbs.7.1068 displayed as A single in. As A heatmap Mathavan et al study in zebrafish chen J, Poskanzer KE, Freeman,... Is central to our understanding of animal development and human disease the segmentation of 98 expression... Transcriptome landscape of zebrafish embryos download pre-packaged data from zebrafish myeloid cells, Verma A, et al basis. All 18 stages are displayed as A heatmap active in developing embryos 3D expression within the of. Disorders and evolutionary theories related to brain and neuronal cell physiology names and gene Ontology.... 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Month: the inner ear in published songbird studies across four days of development using duplicate that! And widely used in vivo model 3D for 9 different genes brain and cell! Information in ZFIN segmentation of 98 zebrafish gene expression atlas expression atlas release May 2017 cell gene patterns. Zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes Yukselen O, Stone,. On Bioconductor Search and download pre-packaged data from expression atlas - A database gene... Three-Dimensional anatomical atlas of vertebrate early development Kirschner MW, Klein AM, 181,415 detected cell nuclei and segmentation... Email updates of new Search results zebrafish myeloid cells, Li R, Verma A, Vellarikal SK, R!

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