RNAquarium

Repository-scale analysis of transcriptomes from zebrafish and their microbes

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Data

Browse, explore, and download all RNAquarium datasets from a single page. Each category provides downloadable files when available.

Metadata

Access and explore comprehensive metadata for all samples and transcripts. Explore all the metadata in this project without downloading anything.

TOOL

RAW FILES

May 2026 curated zebrafish metadata with SeqDetective and technology updates

Assembled Transcripts

Visualize assembled transcripts and download transcript sequences and taxonomy metadata from zebrafish RNA-seq experiments.

RAW FILES

Non-host assembled transcript sequences FASTA

Non-host taxonomy hits metadata

Gene Expression

Analyze and visualize gene expression data across samples.

RAW FILES

All quantification matrix

Sample annotations AnnData

Corrected host gene expression matrix with UMAP data

Models & Embeddings

Explore machine learning models and gene embeddings.

RAW FILES

RNAquarium second-to-last layer embeddings

ESM2 15B embeddings with gene names

Sample UMAP

Explore sample-level RNA sequencing data in the custom UMAP tool. The corrected host gene expression matrix in Gene Expression includes the UMAP data.

TOOL