Gene expression
What marks definitive endoderm progenitors in hESCs?
Open access · cc by · source: Europe PMC
Single-cell RNA-seq separates definitive endoderm progenitors and links metabolism/hypoxia to DE differentiation.
Study at a glance
- Design
- Animal / in-vitro — scRNA-seq of H1/H9 progenitors and oxygen-condition tests during definitive endoderm differentiation
- N
- N=1018 · 1,018 single cells analysed (including H1 n=212, H9 n=162, HFFs n=159)
- Population
- Human embryonic stem cells and lineage-specific progenitors
- Outcome
- Single-cell regulators and hypoxia effects on definitive endoderm differentiation
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
PC5 separates DE cells; metabolism genes load on that axis; severe hypoxia (1.5% O2) increases CXCR4+ DE-like cells versus higher O2.
Methodology
Profiled lineage-specific progenitors from H1 hESCs by scRNA-seq and tested oxygen conditions during DE differentiation.
Limitations
Does not provide a full clinical protocol for organ replacement therapy.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
Multiple empirical papers in this library examine gene expression with mechanistic biological findings.
Evidence for the claim as stated.
PC5 separates DE cells; metabolism genes load on that axis; severe hypoxia (1.5% O2) increases CXCR4+ DE-like cells versus higher O2.
Evidence for the claim as stated.
Systems and scales differ across gene expression studies (species, tissues, methods), so mechanisms should not be over-generalised.
Evidence for the claim as stated.
Three papers in this method list barely use knockout or knockdown. APEX2 proximity labelling mapped 22 outer-mitochondrial and 72 ER-membrane proteins facing the cytosol; scRNA-seq of H1 hESC progenitors found that 1.5% O2 increases CXCR4+ definitive-endoderm-like cells; caveolar-coat work purified caveolin–cavin complexes. Those are maps and culture conditions, not gene deletions.
Evidence for the claim as stated.
Lexicon hits also disagree with the genuine KO/KD set. APEX2 inventories, hESC scRNA-seq under hypoxia, and caveolar stoichiometry do not perturb named genes, so they cannot be cited as knockdown evidence for trafficking proteins they merely list.
Evidence for the claim as stated.
Many papers in the CRISPR index mention CRISPR or Cas proteins in passing while the actual experiment is something else (APEX2 proximity labelling, pan-genome presence/absence, ChIP-seq of histone acylations, scRNA-seq of endoderm). Those hits show why a body-count lexicon over-recruits; they are not additional editing results.
Evidence for the claim as stated.
In H1 human embryonic stem-cell differentiation, severe hypoxia (1.5% O2) increased CXCR4+ definitive-endoderm-like cells versus higher oxygen, while scRNA-seq PC5 separated DE cells with metabolism genes loading on that axis. CXCR4 flow is a surface-marker gate on a differentiation protocol, not a clinical organ-replacement recipe.
Evidence for the claim as stated.
Flow is counting different objects. Salmonella work counts persistent bacteria inside LN DCs (50–1,000, lumen clear at 3 h); hESC work counts CXCR4+ DE-like cells under 1.5% O2; TB work profiles PD-1+ T cells in 35 human lungs. Those gates are not one 'immune panel'.
Evidence for the claim as stated.
scRNA-seq can separate definitive endoderm progenitors and point to hypoxia effects in hESC cultures.
In human ES differentiation, scRNA-seq separated definitive endoderm progenitors (PC5 signature) and motivated severe hypoxia experiments that increased CXCR4+ DE-like cells.
Evidence for the claim as stated.
In vascularized cortical organoids, scRNA-seq tracks neurogenesis and vessel-related programs.
Single-cell RNA-seq of vOrganoids illustrated robust neurogenesis and differentially expressed genes related to blood-vessel morphogenesis, alongside synaptic physiology and transplant vessel formation.
Scope note — different developmental lineage question
Limits the claim's scope: a different population, assay, or outcome.
hESC endoderm time courses, brain organoid atlases, and CRC tumor atlases all use scRNA-seq without answering the same biological question—do not average their findings into one ‘scRNA-seq result.’
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
Systems and scales differ across gene expression studies (species, tissues, methods), so mechanisms should not be over-generalised.
Lexicon hits also disagree with the genuine KO/KD set. APEX2 inventories, hESC scRNA-seq under hypoxia, and caveolar stoichiometry do not perturb named genes, so they cannot be cited as knockdown evidence for trafficking proteins they merely list.
- Supports · Mapping the faces of mitochondria and ER
- Supports · What proteins build the caveolar coat?
Flow is counting different objects. Salmonella work counts persistent bacteria inside LN DCs (50–1,000, lumen clear at 3 h); hESC work counts CXCR4+ DE-like cells under 1.5% O2; TB work profiles PD-1+ T cells in 35 human lungs. Those gates are not one 'immune panel'.
- Supports · LN DCs shelter antibiotic-tolerant Salmonella
- Supports · PD-1 blockade reactivates TB via TNF
hESC endoderm time courses, brain organoid atlases, and CRC tumor atlases all use scRNA-seq without answering the same biological question—do not average their findings into one ‘scRNA-seq result.’
Related papers in this topic
Same topic cluster — not a recommendation engine.