RNAquarium: an archive-scale atlas of zebrafish gene expression coupled with pan-taxonomic profiling reveals diverse viral drivers of transcriptomic states

Authors

Aniseia, Y., Waltari, E., Huang, H., Lima, L., Rahman, G., Frank, M., Zhou, A., Kim, Y.-J., Paras, J., Baker, S., Senbabaoglu, Y., Peng, D., Balla, K.

Abstract

Zebrafish RNA-seq studies span diverse developmental, physiological, and disease contexts, yet most analyses remain confined to individual experiments and disregard the non-zebrafish component of the data. We present RNAquarium, a scalable framework for joint transcriptomic and metatranscriptomic analysis of RNA-seq data and apply it to all publicly available zebrafish RNA-seq datasets in the Sequence Read Archive. This resource captures transcriptomic structure across development and tissues, reveals diverse microbial and viral associations, and identifies previously undescribed zebrafish viruses including a close relative of human influenza B virus linked to distinct host transcriptional states. We further demonstrate that archive-scale transcriptomes can support foundation-model training and prediction of infection-associated transcriptomic signatures. RNAquarium provides an open framework and interactive portal for exploring the breadth of zebrafish gene expression patterns and associated taxa profiled across a large research community and establishes a generalizable strategy for integrating transcriptomic and metatranscriptomic analyses across the diversity of life represented in public sequencing archives.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 20 Jun 2026.

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