With an increasing number of transcriptome studies in fish, large amounts of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fishes.   

Relevant transcriptome databases have been reported in human, mouse, plant, etc., providing extensive RNA-seq, scRNA-seq and spatial transcriptome information, but no relevant database has been reported in fish. A significant volume of valuable genomic and transcriptomic data in fish remains untapped within sequencing datasets, with only a fraction scattered across various comprehensive databases. As a result, there is a lack of available online resources.

Recently, a research group led by Prof. XIA Xiaoqin from the Institute of Hydrobiology (IHB) of the Chinese Academy of Sciences collected the relevant data of fish transcriptome and created three related databases - the bulk RNA-seq database FishGET (Fish Transcriptome and Expression Database), the scRNA-seq database FishSCT (Fish Single-Cell Transcriptome Database), and the spatial transcriptome database FishSED (Fish Spatial Expression Database). The studies were published in iScience and Science China Life Sciences. (FishGET, FishSCT, FishSED).  

FishGET contains a total of 1362 RNA-seq paired-end data (including mRNA and lncRNA) from 97 different studies about eight fish species, including zebrafish, grass carp and rainbow trout. Transcript assembly, weighted gene co-expression network analysis (WGCNA), function annotation, neighbor location annotation, lncRNA type annotation, and homology annotation have been made on the data. FishGET provides a variety of dynamic interactive visualization services, and displays the gene expression and co-expression networks in various tissues and organs at different developmental stages of fish.

FishSCT contains scRNA-seq data of nine fish species and is the most complete online resources for zebrafish single cell transcriptome data. Based on 129 datasets from 44 studies published before October 2022, 964 marker genes and 26,965 potential marker gene information, as well as expression profiles at single-cell resolution, have been obtained through unified analysis, involving 245 cell types. The zebrafish data formed the backbone of the database, comprising 848 markers and 13,800 potential marker gene information for 222 cell types and covering tissues or organs at various stages of the zebrafish's growth and development. FishSCT provides a user-friendly web interface to browse the expression patterns and marker information of target genes and the function of cell type identification. 

FishSED is a database providing spatial transcriptome data in fish. It collated the published raw data about the spatial transcriptome of zebrafish, covering spatial expression profiles of 56 datasets from 10 projects. The sample types include embryos and several other tissues at all stages of development. 3D gene expression profiles covering five sequencing techniques have been obtained, and an interactive fish spatial transcriptome data platform has been established. FishSED provides different visualization services according to different sequencing technologies, and can search and map multi-gene expression patterns across datasets for comparative analysis. 

The above three databases provide the spatial and temporal expression profiles of various experimental types during the entire developmental stage, which can provide reference for the study of gene function in fish. 

Fish Gene Expression Databases (Image by IHB)