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Genomic Resources for Zebrafish

Genomic Resources for Zebrafish

Oct 06, 2021

Table of Contents

Chemical Phenomics Initiative

https://my.vanderbilt.edu/chemicalphenomics / 

As a way of introduction, I do chemical genetics of zebrafish early development. https://medschool.vanderbilt.edu/chaz-hong-lab /

Briefly, in a manner analogous to classic mutagenesis screens, we conduct high-throughput chemical screens using zebrafish to discover small molecules that specifically perturb embryonic pattern formation.  Using the interdisciplinary chemical genetic approach, we have discovered exquisitely selective modulators of the Bone Morphogenetic Protein (BMP), Wnt and Hedgehog pathways, as well as important new signaling components that direct early vertebrate development. For example, I discovered dorsomorphin, the first small molecule inhibitor of BMP signaling. The technology from this effort is nearing an Investigational New Drug (IND) stage for several devastating human diseases, such as fibrodysplasia ossificans progressiva, and incurable pediatric cancers.

Importantly, from this effort, we also have discovered many compounds that have really interesting effects on zebrafish embryos, but we don’t know the mechanism of action. I hope to initiate a “crowd sourcing” to accelerate discovery and translation.  

Please do not hesitate to contact me with questions about this effort and how it might benefit the zebrafish community. I look forward to hearing from you.

Genome and Map Resources

The Sanger zebrafish homepage hosts all of the efforts of the zebrafish genome sequencing project, including the whole genome sequencing and assembly project with automated annotation in Ensembl and the clone mapping and sequencing project with manual annotation in Vega.

This site allows browsing of zebrafish BAC and PAC clones that were sequenced, analysed and manually annotated within the Sanger zebrafish genome project. Vega includes

For Blast searches against all finished and unfinished clones go here.
The manual annotation is a joint effort between the Sanger Institute and ZFIN.

This site allows browsing of the latest zebrafish whole genome assembly Zv9

Additional DAS tracks with SNP and indel analysis derived from the comparison of the whole genome shotgun reads are available. Ensembl also offers completely customizable downloads with EnsMart
You can search Ensembl with BLAT.

Additional services available at the Sanger Institute

  • Zebrafish Genome Browser at UCSC:

    A joint collaboration between UCSC and the Zebrafish Genome Initiative at Children's Hospital Boston provides several useful tracks of genome data, including:

          Custom annotation tracks for the zebrafish research community include:

           The UCSC Browser for the Tropical 5D Zebrafish Line T5D (also known as Microsporidia Free 5-D line SPF 5-D)

  • Zebrafish Genome Resources at NCBI:

    This page provides information about genomic resources available from NCBI and the zebrafish research community, including sequence, mapping, clone information, and NCBI's independent gene annotation.

A community resource for Zebrafish Genomics.

Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S. FishMap Zv8 update--a genomic regulatory map of zebrafish. Zebrafish. 2010 Jun;7(2):179-80.

Meli R, Prasad A, Patowary A, Lalwani MK, Maini J, Sharma M, Singh AR, Kumar G, Jadhav V, Scaria V, Sivasubbu S. FishMap: a community resource for zebrafish genomics. Zebrafish. 2008 Summer;5(2):125-30.

  • Zebrafish BLAST server at MGH:

    MGH site provides a BLAST search of a gene or marker of interest to the assembled sequence contigs of the zebrafish genomic shotgun sequence from the Sanger project.

Primers

MGH site offers this tool which searches for a supercontig, scaffold, or finished BAC clone by name or accession number, derives all di- and tri- nucleotide repeat sequences in the supercontig, masks the sequence around the repeats for larger zebrafish repetitive sequences and then designs unique sequence primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects. This site also offers a tool to search for marker primer pairs by chromosome coordinates (3MB chromosome segments max.)

The qPrimerDB database (real-time quantitative PCR Primer Database), https://biodb.swu.edu.cn/qprimerdb) is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 516 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice, and maize. The qPrimerDB provides an interactive and information-rich web graphical interface to display search and BLAST results as table-based descriptions and associated links. In this database, we provide 9,273,735 of the best primer pairs for each gene based on primer pair coverage (PPC), as well as 68,653,054 alternative gene-specific primer pairs, which can be conveniently batch downloaded. We validated the specificity and efficiency of the qPCR primer pairs for 66 randomly selected genes in six different organisms through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be updated routinely.

Microarrays

The Trans-NIH Zebrafish Genome Initiative at Children's Hospital Boston aims to annotate zebrafish genes with human known genes for functional and comparative studies. This website provides a web service for retrieving annotated zebrafish genes represented on Affymetrix Zebrafish Genome Arrays and Roche-NimbleGen Zebrafish Expression Arrays to the research community.

  • Microarray expression at ZF-Espresso

  • Zebrafish Oligonucleotide Arrays :

The Norwegian Microarray Consortium offers their array products for academic use to customers world wide. One limitation is oligonucleotide arrays, which cannot provided to users in the US and Japan, due to licensing conditions. A moderate license fee will be added to the base price for oligonucleotide arrays sold to users in the UK, France, Germany, Italy, Austria, Belgium, Sweden, Switzerland, Luxembourg, and The Netherlands.

 

cDNA and EST Resources

NIH initiative for production of full length sequences and cDNA clones.
1819 ZGC clones recloned in pENTR223.1 In May 2008, ZGC has added 1819 full length ZGC clones recloned into a Gateway Entry vector (pENTR223.1;) for expression analysis and other applications.
These clones can be found by searching Entrez nucleotide for "NIH_ZGC_36".

The DFCI Zebrafish Gene Index (ZGI) integrates research data from international zebrafish gene research projects and represents a non-redundant view of all zebrafish genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.

This database consists of 4694 contigs or singletons obtained from ~18000 reads of cDNAs that were isolated from the microdissected otocysts of zebrafish embryos at 20-30 hours postfertilization, following subtraction with a pool of liver cDNAs from adult fishes.

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