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. 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. Epub 2011 Sep 7. We provide a methodology to construct, visualize and analyze a gene expression atlas composed of templates at various stages of vertebrate early development. (A) A screenshot from Expression Atlas release May 2017. 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. 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. You will find an overview image for each stage, with links (click at numbers on image) to images of the sections. Copyright 2021 ZEBrA  All rights reserved. Genes with highly differential expression patterns are then hybridized to several (4-9) levels (~0.2 - 4.0 mm from midline), while genes with non-differential patterns are hybridized to 2-3 levels (~1.0 and 2.4 mm from midline), focusing on documenting expression in song nuclei. Chen J, Poskanzer KE, Freeman MR, Monk KR. 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. eCollection 2020. From whole-mount to single-cell spatial assessment of gene expression in 3D. zfRegeneration - A database for gene expression profiling during regeneration. 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. 2020 Oct 23;3(1):602. doi: 10.1038/s42003-020-01341-1. The Zebrafish scRNAseq atlas should offer the ability to produce accurate gene expression profiles for cell types of interest at multiple developmental stages. Would you like email updates of new search results? We welcome your input and comments. Here we applied single-cell … 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. 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 Relative gene expression levels (FPKM) across all 18 stages are displayed as a heatmap. 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. Cell type ... History of the Human Protein Atlas: read more. Labeled series: these series contain annotated slides: During hindbrain development in zebrafish, proneural gene expression becomes confined to zones flanking the segment boundaries, with low expression in hindbrain boundary cells and also in rhombomere centres (Amoyel et al., 2005; Cheng et al., 2004; Gonzalez-Quevedo et al., 2010). 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 automatic quantification and registration strategy to create a gene expression atlas of zebrafish embryogenesis. The generated database allows easy access and retrieval of sequencing data from zebrafish myeloid cells. zfRegeneration - A database for gene expression profiling during regeneration. Here, we described a reduced transcriptome atlas (RTA) approach which integrates transcriptomic data sets and a comprehensive panel of genes generated to represent neurogenesis and the early neuronal development of zebrafish, to determine the potential neurodevelopmental toxicities of environmental chemicals. 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. 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. 2013 May 20;8(5):e64058. 2011;7(7):1068-76. doi: 10.7150/ijbs.7.1068. Fastrès A, Pirottin D, Fievez L, Marichal T, Desmet CJ, Bureau F, Clercx C. Front Immunol. (A) A screenshot from Expression Atlas release May 2017. 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 to empowersystematic interrogations of vertebrate development and disease. Recent news. 2019 Oct 7;9(10):3439-3452. doi: 10.1534/g3.119.400402. Explore the expression patterns of genes that are markers of specific brain structures in zebra finches and in mammals (based on the Allen Institute's Mouse Brain Atlas). 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. Educational videos: Journey into the body: SARS-CoV-2. EMBL-EBI Expression Atlas, an open public repository of gene expression pattern data under different biological conditions Explore the expression patterns of markers of specific nuclei in the zebra finch song system. The zebrafish genome is highly similar to the human genome and there are orthologs for 70% of the human genes .  |  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. Comput Struct Biotechnol J. 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. 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. Furthermore, gene expression index (GEI) analysis demonstrated that a gene panel with 300 genes was sufficient to effectively characterize and cluster chemicals and therefore offer an efficient and cost-effective tool for the prioritization of neurotoxicants. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Here, we investigate the expression of these genes and others during zebrafish osteoblastogenesis. Sci. Using poly(A) pulldown stranded RNA-seq and a 3' end transcript counting method we characterise temporal expression profil … The ZFIQ (Zebrafish Image Quantitator) software toolkit provides a set of image analysis tools for quantitative, reproducible and accurate interpretation of zebrafish imaging data. Thu, 21 Jan 2021 Movie of the month: the inner ear. 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). 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. Crossref . 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. 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. This chapter puts our selection of gene expression patterns into a general theoretical framework of zebrafish brain secondary neurogenesis. NIH Farrell et al. doi: 10.1371/journal.pone.0064058. 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