zfishbook: connecting you to a world of zebrafish revertible mutants

Abstract

zfishbook is an internet-based openly accessible database of revertible protein trap gene-breaking transposon (GBT) insertional mutants in the zebrafish, Danio rerio. In these lines, a monomeric red fluorescent protein (mRFP) is encoded by an artificial 3' exon, resulting in a translational fusion to endogenous loci. The natural transparency of the zebrafish embryo and larvae greatly facilitates the expression annotation of tagged loci using new capillary-based SCORE imaging methods. Molecular annotation of each line is facilitated by cloning methods such as 5'-Rapid Amplification of cDNA Ends (RACE) and inverse polymerase chain reaction (PCR). zfishbook (http://zfishbook.org) represents a central hub for molecular, expression and mutational information about GBT lines from the International Zebrafish Protein Trap Consortium (IZPTC) that includes researchers from around the globe. zfishbook is open to community-wide contributions including expression and functional annotation. zfishbook also represents a central location for information on how to obtain these lines from diverse members of the IZPTC and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information.

Figure 1.

Example GBT summary block—GBT0141. At the top of each GBT line digital notebook is a summary block. The summary block contains the following elements. (A) Specific GBT line information including the official GBT line designation, inventory status, source laboratory, mutagenesis vector used, tagged gene name and status, alternate names from the source laboratory and the official ZFIN allele designation. (B) Expression and phenotype data including a link to the line's media gallery, a list of annotated ZFA Ontology tags, and a description of any known phenotype(s). (C) Links to molecular data including sequence tags, external database links and additional molecular information that includes primer sequences for linkage analysis and quantitative measurement of knockdown. (D) A link to request the line.

Figure 2.

Example GBT expression summary—GBT0141. When image cataloging is completed for a GBT line, an expression summary is placed below the summary block. The expression summary is a grid of flattened z-stack images, specifically maximal image projections of a z-stack. The images from 2 (2DPF) and 4 (4DPF) days post-fertilization are arranged in vertical columns with the dorsal (D), sagittal (S) and ventral (V) images arranged in rows. This allows for quick viewing of the expression pattern, facilitating review of GBT lines for mRFP patterns of interest. By simultaneously viewing and comparing expression in different planes, some reconstruction of the three-dimensional expression pattern is possible.

Figure 3.

Example of ZFA-tagged image—GBT0141, 4DPF, Sagittal. (A) This image has been tagged five times with our ZFA image tagging tool. Although, tagging requires a user login, viewing annotations is available to both unregistered and registered users. When viewing an image in the media gallery, the image tags appear as white rectangles over an mRFP expression domain. When hovering over the tag with the cursor, the rectangle turns yellow and the image tag is displayed. In this example, the cursor is hovering over the image tag over the eye that is part of both the head and the visual system. (B) A direct link to the ZFA lookup tool on zfishbook is below every image, as well as a link to send an email to question the annotation of the image. Only ZFA terms can be used to annotate images on zfishbook. (C) All the ZFA image tags become part of the image's keywords.