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.
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.
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