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bioRxiv · 10.1101/2022.09.21.508858

FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome

Xia, X.-Q.·Guo, C.·Ye, W.·You, D.·Zhang, W.·Cheng, Y.·Shi, M.
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Abstract

With the advancement of single-cell sequencing technology in recent years, an increasing number of researchers have turned their attention to the study of cell heterogeneity. In this study, we created a fish single-cell transcriptome database centered on zebrafish (Danio rerio). FishSCT currently contains single-cell transcriptomic data on zebrafish and 8 other fish species. We used a unified pipeline to analyze 129 datasets from 44 projects from SRA and GEO, resulting in 964/26,965 marker/potential marker information for 245 cell types, as well as expression profiles at single-cell resolution. There are 117 zebrafish datasets in total, covering 25 different types of tissues/organs at 36 different time points during the growth and development stages. This is currently the largest and most comprehensive online resource for zebrafish single-cell transcriptome data, as well as the only database dedicated to the collection of marker gene information of specific cell type and expression profiles at single-cell resolution for a variety of fish. A user-friendly web interface for information browsing, cell type identification, and expression profile visualization has been developed to meet the basic demand in related studies on fish transcriptome at the single-cell resolution.

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Xia, X.-Q., Guo, C., Ye, W., You, D., Zhang, W., Cheng, Y., Shi, M.. 2022-09-22. FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. https://doi.org/10.1101/2022.09.21.508858

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