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tooluniverse-stem-cell-organoid

Analyzes stem cell pluripotency, differentiation pathways, and organoid models using ToolUniverse biomedical tools.

1.7k|254|Updated Mar 3, 2025
Search Tags:#differentiation#disease modeling#ipsc#cellmarker#organoid#pluripotency#stem cell
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-stem-cell-organoid
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-stem-cell-organoid
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-stem-cell-organoid
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-stem-cell-organoid

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires cellxgene-census.

What problem does it solve?

Designing iPSC differentiation protocols and evaluating organoid models requires navigating scattered marker databases, signaling pathway knowledge, and atlas datasets, which is slow and error-prone when done from memory.

Core Features & Use Cases

  • Marker-Based Cell Identity Verification: Query CellMarker for validated pluripotency markers (OCT4, SOX2, NANOG) and lineage-specific markers to confirm cell identity.
  • Differentiation Pathway Analysis: Look up WNT, Notch, BMP, FGF, Hedgehog, and Hippo signaling pathways via KEGG and Reactome to design protocols that recapitulate developmental signaling.
  • Organoid Fidelity Assessment: Score organoid models on cell diversity, architecture, function, and maturation, with evidence grading from T1 (clinical) to T4 (computational).
  • Use Case: A researcher designing a neural differentiation protocol from human iPSCs uses this Skill to retrieve ectoderm markers, confirm dual SMAD inhibition as the correct pathway, and find reference single-cell datasets in CELLxGENE for benchmarking.

Quick Start

Use the stem cell organoid skill to design an iPSC-to-cardiomyocyte differentiation protocol and identify the markers needed to verify each stage.

Frequently Asked Questions about tooluniverse-stem-cell-organoid

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I verify iPSC pluripotency markers?▼

Verify pluripotency by confirming co-expression of OCT4 (POU5F1), SOX2, and NANOG, plus surface markers SSEA-4 and TRA-1-60 for human cells. Use CellMarker_search_by_cell_type to retrieve the full validated marker set rather than relying on memory.

How to design an iPSC differentiation protocol for a target cell type?▼

Design protocols by mimicking the embryonic signaling pathway that generates the target cell type in vivo. For example, neural induction uses dual SMAD inhibition, while cardiomyocytes require WNT activation followed by WNT inhibition. Look up pathways with kegg_search_pathway.

What tools find stem cell single-cell reference datasets?▼

Use CELLxGENE_get_census_versions to discover Census releases, hca_search_projects for Human Cell Atlas organoid projects, and GEO_search_rnaseq_datasets for published RNA-seq studies. Note that CELLxGENE requires the cellxgene-census Python package.

Can mouse and human stem cell protocols be used interchangeably?▼

No, mouse and human stem cells have different signaling requirements. Mouse naive pluripotency depends on LIF/STAT3 signaling, while human primed pluripotency requires FGF/ERK signaling, so protocols are not interchangeable between species.

What are the limitations of organoid disease models?▼

Most organoids resemble fetal rather than adult tissue, so maturation state must be assessed before drawing disease conclusions. Organoids also show batch variability between iPSC lines and passages, and may lack rare cell types or proper architecture.

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