gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development
- 1Chan Zuckerberg Biohub San Francisco
Abstract
Single-cell RNA-sequencing (scRNA-seq) atlases of zebrafish development have catalogued marker genes for hundreds of cell types, but transcriptomic data alone cannot reveal their expression patterns in the embryo. The systematically annotated Thisse high-throughput whole-mount in situ hybridization (ISH) collection at ZFIN provides spatial expression data across twelve developmental stages, yet the ZFIN web interface is organized around individual genes, making side-by-side cross-gene comparison laborious. We present gene2fish, a web application that displays ISH images from the Thisse dataset, linked directly to their ZFIN records, in a gene-by-developmental-stage grid. With gene2fish, researchers can quickly explore and validate the spatial expression of marker gene lists, and find the genes annotated to specific anatomical structures across developmental time. The application is part of Zebrahub and is freely available at https://zebrahub.sf.czbiohub.org/gene2fish.
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BibTeX
@misc{janssen2026gene2fish,
title = {{gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development}},
author = {V. Janssen and W. D. F. Rutes and L. Lima and K. Awayan and B. Iovino and L. A. Royer},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.16.759755},
url = {https://www.biorxiv.org/content/10.64898/2026.10.16.759755v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - gene2fish: a multi-gene spatial expression browser for in situ hybridization data across zebrafish development
AU - V. Janssen
AU - W. D. F. Rutes
AU - L. Lima
AU - K. Awayan
AU - B. Iovino
AU - L. A. Royer
PY - 2026
DA - 2026/10/16
PB - bioRxiv
DO - 10.64898/2026.10.16.759755
UR - https://www.biorxiv.org/content/10.64898/2026.10.16.759755v1
AB - Single-cell RNA-sequencing (scRNA-seq) atlases of zebrafish development have catalogued marker genes for hundreds of cell types, but transcriptomic data alone cannot reveal their expression patterns in the embryo. The systematically annotated Thisse high-throughput whole-mount in situ hybridization (ISH) collection at ZFIN provides spatial expression data across twelve developmental stages, yet the ZFIN web interface is organized around individual genes, making side-by-side cross-gene comparison laborious. We present gene2fish, a web application that displays ISH images from the Thisse dataset, linked directly to their ZFIN records, in a gene-by-developmental-stage grid. With gene2fish, researchers can quickly explore and validate the spatial expression of marker gene lists, and find the genes annotated to specific anatomical structures across developmental time. The application is part of Zebrahub and is freely available at https://zebrahub.sf.czbiohub.org/gene2fish.
ER -