# nucleotide_archive_mcp

> Use this tool when you need to search and access RNA sequencing datasets from the European Nucleotide Archive (ENA) for bulk, single-cell, and spatial transcriptomics research. It solves problems related to data discovery, filtering, and download, supporting advanced queries and bulk data retrieval. The tool accepts search queries and filtering parameters as input and returns relevant RNA sequencing datasets for download and further analysis.

Canonical page: https://skillsregistry.net/skills/biocontext-ai-nucleotide-archive-mcp  
JSON: https://api.skillsregistry.net/v1/skills/biocontext-ai-nucleotide-archive-mcp

## Description

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.

## Trust

- **Trust score (0–1):** 0.68
- **Verification tier:** scanned
- **Last scanned:** 2026-08-31

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** search
- **Updated:** 2026-08-31

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/pxjoc2q2mt)
- **Repository:** <https://github.com/biocontext-ai/nucleotide_archive_mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "biocontext-ai-nucleotide-archive-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/biocontext-ai-nucleotide-archive-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/biocontext-ai-nucleotide-archive-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt