MCP server for searching European Nucleotide Archive (ENA) datasets. Find RNA-seq studies, retrieve metadata, and discover related publications to validate research hypotheses.
Wellknown found it in public sources; nobody has proven control of it yet. Claiming takes one click if the repository is under your GitHub account, or a small file on your domain otherwise. Verified owners get the badge, 15-minute checks, status alerts, edits that outrank crawled data, and a ranking boost.
Agents can do it too: POST https://wellknown.network/api/v1/claims with {"agent":"nucleotide-archive-mcp","method":"well_known_file"} — machine-readable steps at claim.json, guide at /docs/claim.
Everything here was measured by our prober or read from a registry. Nothing is self-reported.
Attributed to the source that supplied each field. Treated as claims, not facts.
# RNA Dataset Search - MCP Server [](https://biocontext.ai/registry) [![Tests][badge-tests]][tests] [![Documentation][badge-docs]][documentation] [badge-tests]: https://img.shields.io/github/actions/workflow/status/biocontext-ai/nucleotide_archive_mcp/test.yaml?branch=main [badge-docs]: https://img.shields.io/readthedocs/nucleotide_archive_mcp A Model Context Protocol (MCP) server for searching and accessing RNA sequencing datasets from the [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena/browser/home). Find publicly available bulk RNA-seq and single-cell RNA-seq datasets to validate research hypotheses or reproduce published analyses. **Optimized for**: Human and mouse disease-related RNA-seq studies with support for bulk, single-cell, and spatial transcriptomics. ## Features - **Disease-Focused Search**: Find datasets by disease, organism, and tissue type - **Advanced Technology Filtering**: - Simple presets: bulk, single-cell, small-rna, ribo-seq, rna-all - Granular control: Filter by 50+ library strategies (RNA-Seq, miRNA-Seq, ChIP-Seq, ATAC-seq, etc.) - Source filtering: TRANSCRIPTOMIC, GENOMIC, METAGENOMIC, etc. - **Common Organism Names**: Use "human", "mouse", "rat" instead of scientific names - **Download Support**: Generate wget/curl scripts for downloading FASTQ files - **Study Metadata**: Retrieve comprehensive metadata including PubMed IDs - **Publication Links**: Discover datasets associated with PubMed publications - **Flexible Queries**: Build custom queries with multiple field conditions - **Field Discovery**: Explore available search and return fields - **Environment Configuration**: Customize API endpoints, timeouts, and logging via environment variables ## Available Tools The MCP server provides 10 specialized tools: ### Search & Discovery …
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Every source is kept verbatim. Field changes are logged as events.