The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index; none of the 15 sources its claims cite is checked for support yet.
Single-cell analysis of mixed-lineage states leading to a binary cell fate choice
Open accessAbstract
Delineating hierarchical cellular states, including rare intermediates and the networks of regulatory genes that orchestrate cell-type specification, are continuing challenges for developmental biology. Single-cell RNA sequencing is greatly accelerating such research, given its power to provide comprehensive descriptions of genomic states and their presumptive regulators. Haematopoietic multipotential progenitor cells, as well as bipotential intermediates, manifest mixed-lineage patterns of gene expression at a single-cell level. Such mixed-lineage states may reflect the molecular priming of different developmental potentials by co-expressed alternative-lineage determinants, namely transcription factors. Although a bistable gene regulatory network has been proposed to regulate the specification of either neutrophils or macrophages, the nature of the transition states manifested in vivo, and the underlying dynamics of the cell-fate determinants, have remained elusive. Here we use single-cell RNA sequencing coupled with a new analytic tool, iterative clustering and guide-gene selection, and clonogenic assays to delineate hierarchical genomic and regulatory states that culminate in neutrophil or macrophage specification in mice. We show that this analysis captured prevalent mixed-lineage intermediates that manifested concurrent expression of haematopoietic stem cell/progenitor and myeloid progenitor cell genes. It also revealed rare metastable intermediates that had collapsed the haematopoietic stem cell/progenitor gene expression programme, instead expressing low levels of the myeloid determinants, Irf8 and Gfi1 (refs 9, 10, 11, 12, 13). Genetic perturbations and chromatin immunoprecipitation followed by sequencing revealed Irf8 and Gfi1 as key components of counteracting myeloid-gene-regulatory networks. Combined loss of these two determinants ‘trapped’ the metastable intermediate. We propose that mixed-lineage states are obligatory during cell-fate specification, manifest differing frequencies because of their dynamic instability and are dictated by counteracting gene-regulatory networks.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
Single-cell RNA-Seq and ICGS resolved nine hierarchical myeloid states and identified prevalent and rare mixed-lineage intermediates during neutrophil-versus-macrophage specification. Irf8 and Gfi1 act as counteracting determinants of a metastable transition state that can be “trapped” by combined loss of both factors.
Key findings
- ICGS resolved nine hierarchically ordered cellular states—HSCP-1, HSCP-2, Meg, Eryth, Multi-Lin*, MDP, Mono, Gran, and Myelocyte—whose inferred developmental order agreed with the experimentally determined hematopoietic sequence.
- A prevalent Multi-Lin* state co-expressed HSCP and myeloid progenitor genes (Ctsg, Mpo, Elane) and the TFs Gata2, Meis1, PU.1, and C/EBPα, with variable priming of megakaryocytic, erythroid, granulocytic, and monocytic genes.
- Rare metastable intermediates expressed low levels of both Irf8 and Gfi1; Irf8hi GMPs were specified monocytic progenitors (CFU-M), Irf8− GMPs contained specified granulocytes (CFU-G) and bipotential progenitors (CFU-GM), and IG2s gave equal proportions of monocytic and granulocytic colonies.
- ChIP-Seq showed Irf8 peaks enriched for EICE motifs co-bound by PU.1, shared Gfi1/Irf8 regions accessible in GMPs, and increased H3K4me2 at shared regions upon Gfi1 loss or Lsd1 inhibition, correlating with enhanced monocytic potential.
Methods
- scRNA-Seq was performed on mouse LSK, CMP, GMP, and LKCD34+ cells using the C1 Single-Cell Auto Prep System; 96 LSK, 96 CMP, 136 GMP, and 66 LKCD34+ libraries were sequenced, with QC failures in 3 LSK, 2 CMP, 4 GMP, and 3 LKCD34+ samples. Additional scRNA-Seq was performed on GG1s, IG2s, and Irf8−/−Gfi1−/− GMP-like cells.
- ICGS used pairwise correlation of dynamically expressed genes and iterative clustering with pattern-specific guide genes, excluding cell-cycle genes; results were compared with six independent computational approaches and annotated using GO-Elite/ImmGen enrichment.
- ChIP-Seq for Gfi1, Irf8, and H3K4me2 was performed in GMPs, with external Cebpα ChIP-Seq and ATAC-Seq data; functional assays included CFU assays, flow cytometry, RT-PCR, and an inducible Gfi1 allele.
Limitations
- The paper does not state a formal limitations section.
- Evident from the text: the study is based on mouse bone marrow populations, and human relevance is not tested.
- Evident from the text: rare intermediates are inferred partly from population frequencies, and the Gfi1-GFP reporter expresses stable GFP, which the authors note can over-estimate Gfi1 expression and likely accounts for higher GFP in GG3s despite very low Gfi1 transcripts.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
75 Own result · 13 Own interpretation · 12 Not checked yet · 7 Own method · 2 No basis given
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similarly, clustering of LKCD34+ cells recreated the entire developmental ordering with granulocytic precursors at one end of the continuum (Extended Data Fig. 6b).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Genetic perturbations and ChIP-Seq revealed Irf8 and Gfi1 as key components of counteracting myeloid-gene-regulatory networks.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, during steady-state myelopoiesis a prevalent mixed-lineage state is encountered that expresses HSCP and myeloid progenitor genes (Ctsg, Mpo, and Elane), while displaying molecular priming of erythrocytic, megakaryocytic, granulocytic and monocytic potentials.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Strikingly, similar binding patterns for Gfi1 and Irf8 were seen on the Irf8, Klf4 and Zeb2 genes (Extended Data Fig. 8a).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Notably, Gfi1 and Irf8, which are required for normal granulopoiesis and monopoiesis, respectively9,11,12,24,25, displayed strong partitioning within granulocyte- versus monocyte-specified cells (Fig. 1f).”
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Gene expression patterns of Csf1r, Flt3 and Cx3cr1 suggested that both CMP and GMP contain macrophage/dendritic cell precursors (MDP: CX3CR1+CD115+CD135+)18, which was confirmed by flow cytometry (Extended Data Fig. 6d–f).”
What the sources say
- Not checked yetcites [18] Auffray, C. et al. CX3CR1+ CD115+ CD135+ common macrophage/DC precursors and the role of CX3CR1 in their response to inflammation. J. Exp. Med. 206, 595–606 (2009) source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Clustering of Pearson-correlation coefficients for ICGS-delineated TF-gene pairs (Fig. 1d, e, Extended Data Fig. 6g–j), revealed three distinct regulatory states within GMPs (Fig. 1e).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Each ICGS-delineated cellular state has an underlying regulatory state characterized by distinct combinations of transcription factors.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Analysis of GMPs using an Irf8-GFP reporter (Fig. 3a) and CD115 (Csf1r) revealed two major Irf8-GMP subpopulations (IG1 and IG3) and a minor intermediate (IG2) (Fig. 3b).”
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Conversely Gfi1 transcripts were anti-correlated with Irf8 and Csf1r (Fig. 3c).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Importantly, loss of either TF reduced the heterogeneity of genomic states manifested at the single-cell level (Fig. 2a).”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 29
- Probably not a substantial claim. 17
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In Csf1r+ GMP, inducing Gfi1 repressed monocytic genes (including Irf8), and induced neutrophil genes in a dose-dependent manner (Fig. 2d).”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“This confirmed an established regulatory relationship (e.g. Irf8-Klf423), and suggested new regulatory interactions (Irf8-Zeb2 and Gfi1-Per3).”
What the sources say
- Not checked yetcites [23] Kurotaki, D. et al. Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation. Blood 121, 1839–1849 (2013) source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“GG2 cells expressed highest levels of Gfi1 and represented specified granulocytic progenitors, while GG3 cells, which expressed highest levels of Irf8 were oppositely specified as monocytic progenitors (Fig. 3f–h).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Genes located near the shared genomic regions were associated with monocytic-dendritic-precursors (ImmGen) or abnormal mononuclear cell morphology (Mouse Phenotype Ontology), and were reciprocally dysregulated in Irf8−/− or Gfi1−/− GMPs (Extended Data Fig. 7f).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Intriguingly, the IG2s, which expressed low levels of Irf8 and Gfi1 (Fig. 3b, c), appeared to represent cells poised to undergo specification as they gave rise to equal proportion of monocytic and granulocytic colonies.”
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In agreement with regulatory state (Fig. 1e) and loss-of-function analyses (Fig. 2a), key TFs were reciprocally altered by increased expression of Gfi1; Klf4, Zeb2 and Irf5 were repressed whereas Ets1 and Per3 were induced.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Notably, Irf8 peaks were enriched for EICE motifs, which are co-bound by PU.126.”
What the sources say
- Not checked yetcites [26] Brass, A. L., Zhu, A. Q. & Singh, H. Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers. EMBO J. 18, 977–991 (1999) source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Gfi1 induction in GMP increased granulocytic and diminished monocytic potential (Extended Data Fig. 8c, d).”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Colony forming unit (CFU) assays demonstrated that Irf8hi GMPs (IG3) were specified monocytic progenitors (CFU-M); whereas Irf8− GMPs (that expressed highest levels of Gfi1) comprised of specified granulocytes (CFU-G) as well as bipotential progenitors (CFU-GM) (Fig. 3d).”
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The remaining two groups of cells expressed low levels of Gfi1 and Irf8 along with the myeloid genes Etv6, Mpo, Elane, Hax1, a subset of these expressed higher levels of Irf8 along with Cybb and Ly6a (Fig. 4a).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“HOPACH generated clusters using ICGS for mouse intestinal organoids1 for the discovery of rare cell populations.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Seurat hierarchical relationships between the predicted cell states, based on 161 differentially expressed genes.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Significant changes in expression of key genes between Irf8−/− versus Irf8-high WT GMP, or Gfi1−/− versus Gfi1-high WT GMP are noted (* p<0.05, ** p<0.01, *** p<0.001 Benjamini-Hochberg adjusted).”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Seurat t-SNE displayed output for the 9 predicted cell states.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We note induction of Irf8 at low levels is associated with loss of the multipotential program but is not accompanied by specification of monocytes.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“HSCP gene expression waned in IG2s and they co-expressed Gfi1 and Irf8.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“HOPACH generated clusters using ICGS for human myoblast differentiation, without inclusion of cell cycle associated genes.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of the 96 LSK, 96 CMP, 136 GMP and 66 LKCD34+ libraries that were sequenced, 3 LSK, 2 CMP, 4 GMP and 3 LKCD34+ samples failed the QC analysis.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“GG2 cells expressed highest levels of Gfi1 and represented specified granulocytic progenitors, while GG3 cells, which expressed highest levels of Irf8 were oppositely specified as monocytic progenitors (Fig. 3f–h).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“To test this, we analyzed IG2s (Fig. 4a, Extended Data Fig. 10i), which lack bipotential progenitors (CFU-GM) and are highly enriched for cells undergoing lineage specification, resulting in CFU-G and CFU-M.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Note that Irf8−/− and Gfi1−/− GMP continue to express non-productive transcripts emanating from the mutant Gfi1 and Irf8 alleles.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The second cluster down regulated most HSCP genes except Gata1 and expressed Gfi1, Il5ra, Prg2 and Epx.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Heatmap of the t-SNE based cell-state ordering and the top 150 most significant RaceID genes associated with each of the 14 k-means clusters.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similarly, an intermediate level of Gfi1 expression is associated with loss of the multipotential program, but a further increase in its expression coincides with neutrophil specification.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These cells were not contaminants as they expressed CD16/32 and CD34 (Extended Data Fig. 9e, f), and corresponded to the bipotential cells (CFU-GM) within the GG1 population (see below).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Cell cycle associated genes were enriched (z-score>1.96) in Gfi1−/− and depleted (z-score <−1.96) in the Irf8−/− GMPs.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“HOPACH generated clusters derived using ICGS for human scRNA-Seq data for pre-implantation embryos and embryonic stem cells.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Single-cell RNA-Seq library fragment distribution before and after optimization reveals an increase in reads that can be mapped to the genome (reads mapping to a single genomic/transcriptomic location using BowTie2/TopHat2; 61.8% before and 83.5% after optimization).”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Lsd1 inhibition results monocytic colony formation and increased Irf8 expression.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We propose that mixed-lineage states are obligatory during cell-fate specification and manifest differing frequencies because of their “dynamic instability”, dictated by counteracting gene-regulatory networks.”
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: Mixed-lineage states reflect molecular priming of developmental potentials by co-expressed alternate-lineage determinants, namely transcription factors.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“mouse manipulations were reviewed and approved by the Children's Hospital Research Foundation Institutional Animal Care and Use Committee (Protocol Number IACUC2013-0090).”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Methods > Mice
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Accordingly, we propose that IG2s manifest “dynamic instability” because of the counter acting functions of Irf8 and Gfi1 and that this metastable state is “trapped” by the elimination of both developmental determinants.”
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: Mixed-lineage states reflect molecular priming of developmental potentials by co-expressed alternate-lineage determinants, namely transcription factors.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Methods > RNA-Seq and ChIP-Seq Data Processing
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For flow cytometric statistics, a t-test was performed from at least 3 independent experiments.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Methods > Flow cytometry and cell sorting
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The oscillatory behavior may be a reflection of partial assembly of counter acting regulatory states or a lack of their stabilization.”
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The Gfi1-GFP reporter expresses a stable GFP, which can over-estimate Gfi1 expression, likely accounting for higher GFP expression in GG3s (Fig. 3f) in spite of very low levels of Gfi1 transcripts (Fig. 3g).”
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Based on its frequency, this state is inferred to be metastable, but could be “trapped” by elimination of counter-acting determinants.”
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The concept of “trapping” of rare developmental intermediates by genetic perturbation is based on the analogy with trapping of unstable transition states in chemical reactions using physico-chemical strategies33.”
What the sources say
- Not checked yetcites [33] Mitchison, T. & Kirschner, M. Dynamic instability of microtubule growth. Nature 312, 237–242 (1984) source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Expression of Flt3, Csf1r and Cx3CR1 identifies MDP, while expression of Batf3 and Ifi205 suggests dendritic cell differentiation.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Correlation between bulk RNA-Seq (TRUseq Stranded mRNA HT kit) for each sorted population compared to average single-cell gene expression values from the same sort (e.g. LSK, CMP, or GMP).”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“In order to identify sub-populations of 3 cells, present at 10%, a minimum of 30 cells was required. For primary discovery analyses n>90 was required.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Methods > RNA-Seq and ChIP-Seq Data Processing
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
In the paper
“In agreement with our previous report that Gfi1 controls two genetically separable programs; granulopoiesis and Hox-based myeloid progenitor proliferation25”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
What the sources say
- Not checked yetcites [25] Holtschke, T. et al. Immunodeficiency and chronic myelogenous leukemia-like syndrome in mice with a targeted mutation of the ICSBP gene. Cell 87, 307–317 (1996) source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This may generate oscillations in the regulatory states of multi- or bi-potential intermediates, resulting in bursts of alternate lineage gene expression.”
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Genes and cells outlined in the dotted box were re-clustered with HOPACH to delineate relationships between monocytic and granulocytic programming among the different indicated cell populations (Fig. 4c).”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper relies on this without support.
The nature of the transition states manifested in vivo and the underlying dynamics of the cell-fate determinants have remained elusive.
“Although a bistable-gene-regulatory network has been proposed to regulate the specification of neutrophils versus macrophages7,8, the nature of the transition states manifested in vivo and the underlying dynamics of the cell-fate determinants have remained elusive.”
The paper relies on this without support.
Each ICGS-delineated cellular state has an underlying regulatory state characterized by distinct combinations of transcription factors.
“Each ICGS delineated cellular state is expected to have an underlying regulatory state characterized by distinct combinations of TFs.”
The paper relies on this without support.
Mixed-lineage states reflect molecular priming of developmental potentials by co-expressed alternate-lineage determinants, namely transcription factors.
“Such mixed-lineage states may reflect molecular priming of developmental potentials by co-expressed alternate-lineage determinants, namely transcription factors.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“As part of the genomics revolution, increasingly accurate deep sequencing and novel methods of cell tracking have revealed hematopoiesis to be more of a continuous and less of a discrete and punctuated process than originally envisioned.”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Olsson et al., 2016
In the citing paper
“Thus, while the continuum model clearly addresses some of the oversimplifications of the classic model of hematopoiesis, gene expression alone may be insufficient to distinguish discrete cell populations and may miss other relevant aspects of biology (Olsson et al., 2016).”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Olsson et al., 2016
In the citing paper
“When computationally reconstructed, single-cell RNA sequencing (scRNA-seq) profiling of the mammalian hematopoietic system typically produces a largely continuous distribution of cells from the earliest HSCs through the characteristic hematopoietic lineages (Nestorowa et al., 2016; Olsson et al., 2016; Paul et al., 2015; Pellin et al., 2019; Tusi et al., 2018; Weinreb et al., 2020).”
From Unraveling Hematopoiesis through the Lens of Genomics (2020) · cites this paper as Olsson et al., 2016
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
“f, Cytospin analysis of eosinophils in GG1 derived CFU from panel i.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
“i, ICGS of GG1 and IG2 cells with those spanning the entire myeloid developmental spectrum (Fig. 1b).”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
“c. Gfi1−/− GMPs show a significant increase in cell cycle-related gene expression compared to wildtype or Irf8−/− GMPs.”
§ Single-cell analysis of mixed-lineage states leading to a binary cell fate choice > Extended Data
“c, Gfi1 (green), Irf8 (blue) and Cebpα (red) ChIP-Seq and RNA-Seq tracks illustrating co-regulation at select loci.”
Citations
Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
Self-citationThe Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., & Rinn, J. L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2859 · Cited by 7,314
Spatial reconstruction of single-cell gene expression data
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055
Orchestrating high-throughput genomic analysis with Bioconductor
Huber, W. K., Carey, V. J., Gentleman, R. C., Anders, S., Carlson, M. R. J., Carvalho, B. S., Bravo, H. C., Davis, S. R., Gatto, L., Girke, T., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3252 · Cited by 3,614
Dynamic instability of microtubule growth
Mitchison, T., & Kirschner, M. (1984) · Nature · doi:10.1038/312237a0 · Cited by 3,337
Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., & Miyawaki, A. (2002) · Nature Biotechnology · doi:10.1038/nbt0102-87 · Cited by 2,769
Jung, S., Aliberti, J., Graemmel, P., Sunshine, M. J., Kreutzberg, G. W., Sher, A., & Littman, D. R. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.11.4106-4114.2000 · Cited by 2,632
Cited by
Sorted by citations
Reversed graph embedding resolves complex single-cell trajectories
Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4402 · Cited by 5,070
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232
Single-cell transcriptional diversity is a hallmark of developmental potential
Gulati, G. S., Sikandar, S. S., Wesche, D. J., Manjunath, A., Bharadwaj, A., Berger, M. J., Ilagan, F., Kuo, A. H., Hsieh, R. W., Cai, S., et al. (2020) · Science · doi:10.1126/science.aax0249 · Cited by 1,571
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457
Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
Ma, S., Zhang, B., LaFave, L. M., Earl, A. S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V. K., Tay, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.056 · Cited by 1,146
Metadata
- Authors
- Olsson, A., Venkatasubramanian, M., Chaudhri, V. K., Aronow, B. J., Salomonis, N., Singh, H., & Grimes, H. L.
- Affiliations
- Cincinnati Children's Hospital Medical Center (US)
- Corresponding author
- Salomonis, Nathan
- Singh, Harinder
- Grimes, H. Leighton
- ORCID
- Venue
- Nature
- Published
- 2016-08-31
- Volume
- 537
- Issue
- 7622
- Pages
- 698-702
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5161694
- OpenAlex
- W2515907404
- Semantic Scholar
- f4cfb99ea0ea2e73c36ba3b1cd57e59bd22bd1d3
- Cited by
- 476
- References
- 50
- Citations by year
- 2026: 11 · 2025: 24 · 2024: 42 · 2023: 44 · 2022: 38 · 2021: 55 · 2020: 78 · 2019: 64 · 2018: 58 · 2017: 59 · 2016: 3
- FWCI
- 31.89
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-04-24)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (UL1TR001425)
- National Heart, Lung, and Blood Institute (R01HL122661)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK090971, P30DK078392)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (P30AR047363)
- National Center for Advancing Translational Sciences
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- cell fate determination, hematopoiesis, single-cell RNA sequencing, IRF8, GFI1, hematopoietic stem cells, myeloid progenitor cells, chromatin accessibility
- MeSH terms
- Interferon Regulatory Factor-8, Animals, Cell Differentiation, DNA-Binding Proteins, Female, Macrophages, Male, Mice, Inbred C57BL, Models, Biological, Neutrophils, Transcription Factors, Sequence Analysis, RNA, Cell Lineage, Gene Expression Profiling, Myeloid Progenitor Cells, Chromatin Immunoprecipitation, Interferon Regulatory Factors, Mice, Gene Regulatory Networks, Single-Cell Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-10, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
