Table of Contents

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• 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:

• • Mapping & Sequencing: Position / Conigs / Scaffolds / RH Map / BAC End Pairs & Singles / Gap / GC Percent
  • Genes & Gene Prediction: RefSeq Genes / Ensembl Genes
  • mRNA & EST: ZF mRNAs & ESTs / spliced ESTs / WZ EST Clusters / nonZF mRNAs
  • Expression & Regulation: Affy ZF
  • Comparative Genomics: Fugu Chain & Net / Human Proteins / HG Blast
  • Variation & Repeats: RepeatMasker / SimpleRepeats

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• • RH Map (about 9K sequences)
  • BAC End Clones (over 288K pairs, 23K singletons)
  • WZ ESTs (43K sequences, 76K alignments, 39K EST alignments)
  • Affymetrix Zebrafish Microarray Probe Alignments (15K probes)
  • Human Protein (over 40K alignments)

• 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.

• SNPFisher : Variant Report Compiler:

  Variation data for FLI, TL, and WIK.  The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser.

  Butler MG, Iben JR, Marsden KC, Epstein JA, Granato M, Weinstein BM. 2015. SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish. Development. 142: 1542-52.

  
  

• FishMap Zebrafish Genomics Knowledge base:

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.

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• BLAST hits of Human Genes from Sanger sequence maintained by Zon lab:

  Each human gene annotated on the Santa Cruz site was compared by BLAST against the Sanger Institute zebrafish genome sequence. These data can be used to help identify zebrafish orthologues of human or Fugu genes.

• 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.

• Tübingen Map of the Zebrafish Genome

• RH, meiotic and integrated maps of the genome:

  Centralized site for all meiotic and radiation hybrid maps of the zebrafish genome.

Primers

• MGH Web-based Tool for Automating Primer Selection:

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•   Hopkins lab large insertional mutagenesis screen database : 

Detailed information on the mutants resulting from the large insertional mutagenesis screen described in Amsterdam, et al. (2004) Identification of 315 genes essential for early zebrafish development. Proceeding of the National Academy of Sciences 101: 12792-12797

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• Zfishbook: real-time database of gene-break transposon mutagenesis projects in the zebrafish (Steve Ekker laboratory).

• Digital Fish: flip trap database and digital atlas (Scott Fraser laboratory).
• CreZoo: database for zebrafish Cre driver and responder lines (Michael Brand laboratory).
• zTrap: Tol2-mediated gene and enhancer traps that express GFP or Gal4 in specific cells, tissues, and organs (Koichi Kawakami laboratory).
• Zebrafish Enhancer Trap Database: Gal4FF enhancer trap lines enriched for brain selective expression maintained at NICHD (Harold Burgess laboratory).
• ZInC: zebrafish insertion mutation collection (Shuo Lin/Shawn Burgess laboratories).
• Engert lab neural enhancer trap line resource: This neural enhancer trap line resource is a collection of Gal4 expressing enhancer trap lines which have been registered to the ZBrain for expression comparison and annotation. Full resolution stacks can be downloaded from the website and lines can be ordered from the Engert lab.

TALENs/CRISPRs

• Feng Zhang

  Michael Boutros lab's

  CRISPR design

  E-CRISP: 

The CRISPR design tool E-CRISP is a web software tool crafted to simplify the process of CRISPR guide selection in an input DNA sequence by (i) discovering possible offtargets genome-wide, (ii) highlighting guides with high target specificity, and (iii) flagging guides with numerous or genic offtargets in target genomes.

• Michael Boutros lab's E-CRISP: 

E-CRISP is a software tool to design and to design and evaluate target sites for use with the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) system. The web application uses fast algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different options of how CRISPR constructs can be used in experimental applications

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 Identifies gRNA target sequences from an input sequence and checks for off-target binding.

• Mojo Hand: 

A TALEN and CRISPR design tool provided by the Mayo Clinic.

• CRISPRz :

CRISPRz is a curated database of validated CRISPR targets in zebrafish maintained by Shawn Burgess' lab at NHGRI/NIH. The database contains target sites from the Burgess lab's large-scale mutagenesis project, as well as those reported in the literature. A search form allows users to search by various identifiers in order to determine if a validated CRISPR target exists for a gene of interest.

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