The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index; 2 of the 8 sources its claims cite were checked for support.
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
Open accessAbstract
Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, reveal gene expression in poorly characterized cell populations and enable the direct and controlled comparison of gene expression in cell types that are shared between tissues, such as T lymphocytes and endothelial cells from different anatomical locations. Two distinct technical approaches were used for most organs: one approach, microfluidic droplet-based 3'-end counting, enabled the survey of thousands of cells at relatively low coverage, whereas the other, full-length transcript analysis based on fluorescence-activated cell sorting, enabled the characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
44 Own result · 26 Own method · 20 Own interpretation · 5 No full text of the sources · 5 No basis given · 1 Supported · 1 Partly supported · 1 Sources not found · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Cluster co-membership alone, however, is insufficient to conclude that two cell populations from different organs represent the same or similar cell types; at any given resolution, unbiased clustering that groups related cells may also group unrelated cells21.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
What the sources say
- Partly supportedcites [21] Freytag, S., Tian, L., Lonnstedt, I., Ng, M. & Bahlo, M. Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. F1000Res 7, 1297 (2018). sourceExperimental — accuracy not yet measured
The Results (Evaluation of clustering tools, Silver standard data; page unavailable) report that most clusters contained mixtures of different inferred cell types, supporting the caution that co-membership alone does not establish cell-type identity. The paper evaluates PBMC datasets, however, and does not test populations from different organs or establish that such populations were grouped together. (LLM, conf=0.84)
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.
- Partly supported
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
“transcriptional heterogeneity of brain endothelial cells”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
plain- 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
“Clusters 1–3 contain mostly single positive T cells (Cd4+ or Cd8a+).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
plain- 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
“a cell population expressing Chodl in limb muscle”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
plain- 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
“Therefore, to determine which clusters are composed of related or unrelated cell types, we computed a heterogeneity score for each cluster (Methods), and found low scores for the biologically sensible clusters discussed above (Extended Data Fig. 9).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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
“To understand which TFs were most informative for specifying cell types, we performed variable selection from random forests (Methods) and determined that 136 TFs are needed to simultaneously define all cell types across all organs (Fig. 5f, Supplementary Table 3).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global transcription factor analysis
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
“The compendium is comprised of single-cell transcriptomic data from 100,605 cells isolated from 20 organs from 3 female and 4 male, C57BL/6JN, 3-month-old mice (10–15 weeks), analogous to 20-year-old humans (Fig. 1).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
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
“The resulting dendrogram closely resembles the dendrogram produced using all expressed genes, indicating that TFs can be used to reconstruct known cell ontology relationships between bulk populations (entanglement = 0.11; Extended Data Fig. 10a).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global transcription factor analysis
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.
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
“Nonetheless, microfluidic droplets identified cell types missed by FACS in both organs, for example kidney mesangial cells, and splenic dendritic and natural killer cells.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
plaindirect- 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
“the expression of MHC class II genes by adult mouse T cells”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
plain- 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.
- Probably not a substantial claim. 27
- It may state two separate claims as one. 45
Every source the paper cites for this claim was checked and supports it.
In the paper
“For each cluster, we provide annotations in the controlled vocabulary of a cell ontology19 to facilitate inter-experiment comparisons.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
What the sources say
- Supportedcites [19] Bakken, T. et al. Cell type discovery and representation in the era of high-content single cell phenotyping. BMC Bioinformatics 18 (Suppl 17), 559 (2017). source
The Background section describes the Cell Ontology as a standard reference nomenclature needed to compare experimental results about cell types. It also says the ontology is used as a reference annotation vocabulary. The citing authors’ statement that they annotated each cluster describes their own work; the citation supports their choice of vocabulary and its purpose. (LLM, conf=0.91)
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.
- Supported
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 transcriptomes were sequenced to an average depth of 814,488 reads per cell (FACS) and 7,709 unique molecular identifiers (UMIs) per cell (microfluidic droplet).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
plain- 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
“The bladder, liver, lung, mammary gland, trachea, tongue, and spleen show nearly twice as many genes detected per cell with FACS compared to microfluidic droplet, whereas heart and marrow show comparable numbers (Extended Data Fig. 5a).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
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.
In the paper
“Their data contains four times as many cells and included several sample types not present in our data, such as neonatal and fetal organs, cell lines, and young adult ovary, peripheral blood, placenta, prostate, small intestine, stomach, testis, and uterus.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
What the sources say
- Not checked — no full text of the sourcecites Han et al.20 Han, X. et al. Mapping the mouse cell atlas by microwell-seq. Cell 172, 1091–1107.e17 (2018). source
plain- 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
“We then determined the TF sets distinguishing each individual cell type from all other cells. These sets vary substantially in size (from 2 to 813 TFs) and are not necessarily unique to each cell type (Fig. 5g–i; Supplementary Table 4).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global transcription factor analysis
plain- 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.
In the paper
“However, our FACS data contains four times as many genes per cell, and we analyzed several organs not present in the Han et al. data set, such as aorta, four brain regions, diaphragm, four fat types, four adult heart chambers, adult skin, tongue, and trachea.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
What the sources say
- Not checked — no full text of the sourcecites Han et al.20 Han, X. et al. Mapping the mouse cell atlas by microwell-seq. Cell 172, 1091–1107.e17 (2018). source
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.
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
“while Cluster 2 contains mostly non-thymic T cells expressing the high affinity IL2 receptor (Il2ra, Il2rb), suggesting they are activated.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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.
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
“Cluster 0 comprises thymic cells undergoing VDJ recombination characterized by RAG (Rag1, Rag2) and TdT (Dntt) expression, and includes uncommitted double positive T-cells (Cd4+, Cd8a+).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
plain- 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
“Cluster 2 contains B cells from fat, limb muscle, lung, spleen, marrow, and liver, but also cells annotated as leukocytes and lymphocytes from the thymus, heart, and limb muscle.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
plain- 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
“As expected, cells from different organs often mixed, with 25 of 54 clusters containing (at least five) cells from distinct organs (Fig. 3).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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
“In contrast, when we repeated the analysis using cell surface markers, RNA splicing factors, or the two groups combined (equivalent to a random set of genes), the entanglement was 0.22, 0.25 and 0.34, respectively, suggesting that none of these molecular classes define cell type to the extent that transcription factors do.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global transcription factor analysis
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
“Finally, Cluster 1 also represents mature T cells, but primarily splenic.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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.
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
“This seems only to occur for populations smaller than ~30 cells, which comprise under 4% of the overall dataset, and represents a lower limit of sensitivity in the current release of data interpretation.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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.
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
“Comparing methods shows organ-specific differences in the number of cells analyzed (Fig. 1b, c), reads per cell (Extended Data Fig. 3a, c) and genes per cell (Extended Data Fig. 3b, d).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
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
“Cluster 4 contains predominantly proliferating thymic T cells which may represent pre-T cells expanding following VDJ recombination.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
hedgedconditional- 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
“Furthermore, with both methods the most abundant cell types analyzed are epithelial cells and leukocytes, although FACS captured a larger diversity of cell types (Extended Data Fig. 4).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
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
“For those cell types captured by both methods, the proportion of each cell type is equivalent (Pearson correlation coefficient: spleen = 0.99, kidney = 0.99).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
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.
It may state two separate claims as one.
In the paper
“For example, the median number of genes detected in bladder is ~4,900 (FACS), 2,900 (droplet), and 900 (microwell-seq), while in kidney it is ~1,400 (FACS), 1,900 (droplet), and 500 (microwell-seq).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
What the sources say
- Not checked — no full text of the sourcecites Han et al.20 Han, X. et al. Mapping the mouse cell atlas by microwell-seq. Cell 172, 1091–1107.e17 (2018). source
plain- 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
“For example, clusters 3 and 48 each contain endothelial cells from five or more organs, and clusters 1 and 24 contain mesenchymal and stromal cells from four or more organs.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
plain- 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
“We clearly observed these markers in several organs including limb muscle (Extended Data Fig. 11), but many showed little evidence of cellular activation.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
boosted- 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
“Dotted horizontal line demarcates the median saturation (~ 0.9).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Extended Data
hedgedn = 55,032- 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 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
“FACS detects more molecules per cell, but fewer cells. Microfluidic droplets detect fewer molecules per cell, but more cells.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Correlating bulk gene expression profiles
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
“Fraction of all detected genes (defined as > 0 reads or UMIs) for each cell, across all organs, detected at increasing read or UMI thresholds for FACS (left; n= 44,949 individual cells), microfluidic droplet (middle; n= 55,656 individual cells), and microwell-Seq (right; n= 28,372 individual cells).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Extended Data
plainn = 44,949- 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.
In the paper
“The number of genes detected (threshold of > 0 reads or UMIs per cell) by FACS (red; n= 21,105 individual cells), microfluidic droplets (green; n = 55,032 individual cells), and microwell-Seq (blue; n= 25,891 individual cells) (Han et al.).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Extended Data
What the sources say
- Not matchedcites Han et al.
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plainn = 21,105- 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.
- Not matched
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
“FACS detects more molecules per cell, but fewer cells. Microfluidic droplets detect fewer molecules per cell, but more cells.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Correlating bulk gene expression profiles
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 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
“Such gene expression profiles largely correlate (Pearson correlation coefficient: 0.74 – 0.90), suggesting that while biases between methods exist, both accurately recapitulate average cell type gene expression profiles.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
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.
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
“All organs used a standard annotation method; an example using liver is contained in the Organ Annotation Vignette.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
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
“This release allows for the exact replication of all results, facilitates in-depth analyses not completed here, and provides a comparative framework for future studies using the large variety of murine disease models.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
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
“In fact, for nearly all reprogramming protocols the TFs used also specified the targeted cell type in our data (Supplementary Table 5), suggesting that our data can inform novel reprogramming schemes.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global transcription factor analysis
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.
In the paper
“Recently, Han et al.20 published a complementary scRNA-seq study across mouse organs.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
What the sources say
- Not checked — no full text of the sourcecites Han et al.20 Han, X. et al. Mapping the mouse cell atlas by microwell-seq. Cell 172, 1091–1107.e17 (2018). 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
“Many of these cell types have not previously been obtained in pure populations, and our data provide a wealth of new information on their characteristic gene expression profiles.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Defining organ-specific cell types
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.
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 is partially explained by cellular abundance and sampling depth (12,333 microfluidic droplet cells vs. 2,216 FACS cells, Supplementary Table 1), and possibly from cell capture and lysis biases between methods.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Methodological comparison
hedgedconditional- 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 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
“Therefore, the dissociation- related satellite cell markers are not universal, and organs likely display unique dissociation-related expression profiles.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
hedged- 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
“While these data are by no means a complete representation of all mouse organs and cell types, they provide a first draft attempt to create an organism-wide representation of cellular diversity.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
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.
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 enabled the direct comparison of cell type composition between organs, and the comparison of shared cell types across organs.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
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
“The fact that most cells of similar cell types cluster together across organs and biological replicates shows that batch effects are not the main source of variance in the dataset.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
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.
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
“3) We annotated cell types using standard cell ontology terms, thereby enabling cross-organ and cross-experiment analyses”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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
“While this is known in human T cells, MHC class II was previously thought restricted to professional antigen presenting cells in mice22.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
What the sources say
- Not checked — no full text of the sourcecites [22] Holling, T. M., Schooten, E. & van Den Elsen, P. J. Function and regulation of MHC class II molecules in T-lymphocytes: of mice and men. Hum. Immunol. 65, 282–290 (2004). 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. 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
“1) All data, analysis, and code is freely available”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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. 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 is a predictable artifact of the annotation scheme: since entire clusters, rather than individual cells, were annotated in each organ, a sufficiently rare cell type that was algorithmically grouped with a more populous cell type will be mis-annotated.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Global clustering across organs
boosteddirectSingle case- 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
“All data, protocols, analysis scripts, and an interactive data browser are publicly shared (http://tabula-muris.ds.czbiohub.org/ ).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
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.
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
“Importantly, the presence of such gene expression changes does not prevent cell type identification or the comparison of cell types across organs.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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.
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
“As the nomenclature is not identical, the analysis was performed between cell types that could be matched with a certain degree of confidence between the three methods (Supplementary Table 2).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Differential expression overlap analysis
hedgeddirect- 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
“Littermates were not recorded or tracked, and mice were housed at the VA VMU for no longer than 2 weeks before euthanasia.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection
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. 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
“Sample wells were then selected if their cDNA concentrations were at least one standard deviation greater than the mean concentration of the blanks.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > cDNA synthesis and library preparation
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.
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
“Sorters were calibrated using FACS buffer every day before collecting any cells, and also after every 8 sorted plates.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > FACS
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.
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
“A similar analysis was done globally for all FACS processed cells and for all microfluidic droplet processed cells to produce an unbiased clustering.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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.
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
“Cells with fewer than 500 detected genes were excluded.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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
“While it is not an exhaustive characterization of all mouse organs, it does provide a rich dataset of the most highly studied organs in biology.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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
“This Tabula Muris, or “Mouse Atlas”, has many uses, including the discovery of new putative cell types, the discovery of novel gene expression in known cell types, and the ability to compare cell types across organs.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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. 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
“Cells with fewer than 50,000 reads (FACS) or 1000 UMI (microfluidic droplet) were excluded.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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. 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
“No sample size choice was performed prior to the study.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection > Sample size, randomization, and blinding
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.
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
“Cells were lexicographically sorted by cell ID to ensure reproducibility.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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.
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
“Cell types were assigned to each cluster using the abundance of known marker genes.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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.
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
“When clusters appeared to be mixtures of cell types, they were refined either by increasing the resolution parameter for clustering or subsetting the data and rerunning steps 3–7.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Clustering
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.
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
“All animal care and procedures were carried out in accordance with institutional guidelines approved by the VA Palo Alto Committee on Animal Research.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection
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.
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
“Sample plates were selected for downstream processing if the mean concentration of blanks (ERCC-containing, non-cell wells) was greater than 0 ng/μl, and, after linear regression of the values obtained from the Quant-iT dsDNA standard curve, the R2 value was greater than 0.98.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > cDNA synthesis and library preparation
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. 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
“Four 10–15 week old male and four virgin female C57BL/6JN (derived from C57BL/6J in 2016) mice were shipped from the National Institute on Aging colony at Charles River to the Veterinary Medical Unit (VMU) at the VA Palo Alto (VA).”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection
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
“Tabula Muris provides a framework and description of many of the most populous and important cell populations within the mouse, and represents a foundation for future studies across a multitude of diverse physiological disciplines.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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.
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
“Randomization and blinding were not performed – the authors were aware of all data and metadata related variables during the entire course of the study.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection > Sample size, randomization, and blinding
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. 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
“Isolating viable single cells from both pancreas and liver of the same mouse was not possible, therefore, 2 males and 2 females were used for each.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection
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.
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
“7) Full-length transcript data makes possible transcription factor, splice variant, and sequence variant analyses.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Discussion
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.
Probably not a substantial claim.
The paper relies on this without support.
It was unknown whether single-cell data from different animals, labs, and techniques could be synthesized into a general resource for biology.
“It therefore remains unknown whether these data can be synthesized as a more general resource for biology.”
The paper relies on this without support.
Comparing data collected from different animals by independent labs with varying experimental techniques is challenging.
“However, while these reports provide valuable characterization of individual organs, it is challenging to compare data collected from different animals by independent labs with varying experimental techniques.”
The paper relies on this without support.
Any individual single-cell sequencing experiment offers only a partial view of cell type diversity within an organism and gene expression within each cell type.
“Any individual single-cell sequencing experiment offers only a partial view of cell type diversity within an organism and gene expression within each cell type.”
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?
The cited source says what the claim attributes to it.
In the citing paper
“A Tabula Muris compendium of single-cell RNA-Seq transcriptome data from 20 mouse organs and tissues (czbiohub.org) (14) revealed that ASGR1 transcripts are exclusively expressed in liver, specifically in hepatocytes (Fig. 1C).”
From Asialoglycoprotein receptor 1 is a novel PCSK9-independent ligand of liver LDLR cleaved by furin (2021) · cites this paper as [14]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Ageing is associated with increased activation of the NLRP3 inflammasome45,107, which is primarily expressed by myeloid immune cells107,108, and a subsequent increase in the expression of IL-1β, which is a major cytokine implicated in promoting ageing-related disease107.”
From NAD+ metabolism and its roles in cellular processes during ageing (2021) · cites this paper as [108]
Experimental — accuracy not yet measuredIn the citing paper
“CD38 expression was specific to adipose-tissue-resident macrophages (CD68+CD64+F4/80+CD11b+CD11c−), not the non-resident population (CD68+CD64+F4/80+CD11b+CD11c+) (Fig. 4h)”
From Senescent cells promote tissue NAD+ decline during ageing via the activation of CD38+ macrophages (2020) · cites this paper as [36]
In the citing paper
“Multiple cells in the brain, including microglia, astrocytes, neurons and endothelial cells, express CD38 (REFS108,160), and treating microglia and astrocytes with inflammatory cytokines induces CD38 expression163,164.”
From NAD+ metabolism and its roles in cellular processes during ageing (2021) · cites this paper as [108]
In the citing paper
“Transcription factors (TFs) have been shown to be the best molecular feature for cell type definition (Schaum et al., 2018).”
From Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei (2019) · cites this paper as Schaum et al., 2018
In the citing paper
“Furthermore, it has been shown that commonly used cell surface markers are limited in their ability to define cell identities (Tabula Muris Consortium et al, 2018).”
From Current best practices in single-cell RNA-seq analysis: a tutorial (2019) · cites this paper as Tabula Muris Consortium et al, 2018
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 transcriptomics of 20 mouse organs creates a Tabula Muris > Abstract
“liver, lung, mammary gland, pancreas, skin, spleen, thymus, tongue, and trachea from the same mouse were immediately processed into single cell suspensions.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Mice and Organ Collection
“Isolating viable single cells from both pancreas and liver of the same mouse was not possible, therefore, 2 males and 2 females were used for each.”
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 transcriptomics of 20 mouse organs creates a Tabula Muris > Extended Data
“a) Barplot showing the heterogeneity score for each cluster containing multiple cell types. b-f) Heatmaps showing the average between-cell-type distances within select clusters”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > Extended Data
“for clusters a) 1, b) 2, c) 3, d) 24, e) 48, f) 53.”
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 transcriptomics of 20 mouse organs creates a Tabula Muris > Single Cell Methods > Calculation of dissociation scores
“For each organ, principal component analysis was performed on a subset of 140 dissociation-related genes23.”
§ Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris > References
“23. Reichardt J & Bornholdt S Statistical mechanics of community detection. Phys Rev E Stat Nonlin Soft Matter Phys 74, 016110 (2006).”
Citations
Cites
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.
Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells
Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124
Gene selection and classification of microarray data using random forest
Díaz‐Uriarte, R., & de Andrés, S. Á. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-3 · Cited by 3,013
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Villani, A.-C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., et al. (2017) · Science · doi:10.1126/science.aah4573 · Cited by 2,413
Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing
Usoskin, D., Furlan, A., Islam, S., Abdo, H., Lönnerberg, P., Lou, D., Hjerling-Leffler, J., Haeggström, J., Kharchenko, O., Kharchenko, P. V., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3881 · Cited by 2,136
Dynamic Pattern Formation in a Vesicle-Generating Microfluidic Device
Thorsen, T., Roberts, R. W., Arnold, F. H., & Quake, S. R. (2001) · Physical Review Letters · doi:10.1103/physrevlett.86.4163 · Cited by 2,052
Statistical mechanics of community detection
Reichardt, J., & Bornholdt, S. (2006) · Physical Review E · doi:10.1103/physreve.74.016110 · Cited by 2,048
A single-cell survey of the small intestinal epithelium
Haber, A. L., Biton, M., Rogel, N., Herbst, R. H., Shekhar, K., Smillie, C., Burgin, G., Delorey, T. M., Howitt, M. R., Katz, Y., et al. (2017) · Nature · doi:10.1038/nature24489 · Cited by 1,750
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Ramsköld, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O. R., Daniels, G. A., Khrebtukova, I., Loring, J. F., Laurent, L. C., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2282 · Cited by 1,609
Research works printed but not linked: 1
- Kassambara, A. Practical guide to cluster analysis in R: unsupervised machine learning 1st edn (CreateSpace, North Charleston, 2017).
Cited by
Sorted by citations
Items 1,901–2,000 of 2,952
Clustering and visualization of single-cell RNA-seq data using path metrics
Manousidaki, A., Little, A. V., & Xie, Y. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012014 · Cited by 4
Aguirre, B., Lin, M., Araujo, E. H., Lu, C.-H., Casero, D., Sun, M. M., Nusinowitz, S., Hanson, J., Calkins, K. L., Gordon, L. K., et al. (2024) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.65.8.10 · Cited by 4
RNA editing in mesothelioma: a look forward
Hariharan, A., Sun, S., Wipplinger, M., & Felley‐Bosco, E. (2020) · Open Biology · doi:10.1098/rsob.200112 · Cited by 4
“Although ADAR1 and ADAR2 are mostly reported as ubiquitous [37], a recent single-cell transcriptome analysis of 20 mouse organs [38] (https://tabula-muris.”
BackgroundLiu, Y., Zhang, Y., Li, S., et al. (2021) · Functional & Integrative Genomics · doi:10.1007/s10142-021-00770-3 · Cited by 4
Kinetic Characterization of ASXL1/2-Mediated Allosteric Regulation of the BAP1 Deubiquitinase
Peng, H., Cassel, J. A., McCracken, D. S., Prokop, J. W., Sementino, E., Cheung, M., Collop, P. R., Polo, A., Joshi, S., Mandell, J. P., et al. (2021) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-0080 · Cited by 4
Single cell biology—a Keystone Symposia report
Cable, J., Elowitz, M. B., Domingos, A. I., Habib, N., Itzkovitz, S., Hamidzada, H., Balzer, M. S., Yanai, I., Liberali, P., Whited, J. L., et al. (2021) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14692 · Cited by 4
MicroRNA-Based Regulation of Embryonic Endothelial Cell Heterogeneity at Single-Cell Resolution
Wälchli, T., Farnhammer, F., & Fish, J. E. (2022) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.122.317400 · Cited by 4
Adamov, A., Secanechia, Y. N. S., & Lancrin, C. (2022) · Scientific Reports · doi:10.1038/s41598-022-16127-0 · Cited by 4
“In the past five years, the tremendous progress in single-cell RNA sequencing (sc-RNA-seq) has allowed the generation of several cell atlases such as the Tabula Muris (Tabula Muris Consortium, 2018).”
BackgroundGranatumX: A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data AnalysisPreprint
Garmire, D. G., Zhu, X., Mantravadi, A., Huang, Q., Yunits, B., Liu, Y., Wolfgruber, T., Poirion, O., Zhao, T., Arisdakessian, C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/385591 · Cited by 5
SHARP: Single-cell RNA-seq Hyper-fast and Accurate Processing via Ensemble Random ProjectionPreprint
Wan, S., Kim, J., & Won, K. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/461640 · Cited by 4
Mapping heritability of obesity by brain cell typesPreprint
Timshel, P. N., Thompson, J. J., & Pers, T. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.27.920033 · Cited by 6
Kirkup, B. M., McKee, A. M., Madgwick, M., Price, C. A., Dreger, S. A., Makin, K. A., Caim, S., Gall, G. L., Paveley, J., Leclaire, C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.07.982108 · Cited by 4
“The top cluster marker genes were compared to cell type marker genes identified in the literature and used for cell-type identification (55-57).”
MethodsinglecellVR : interactive visualization of single-cell data in virtual realityPreprint
Stein, D. F., Chen, H., Vinyard, M. E., Qin, Q., Combs, R. D., Zhang, Q., & Pinello, L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.30.229534 · Cited by 4
In-depth analysis reveals complex molecular etiology of idiopathic cerebral palsyPreprint
Li, N., Zhou, P., Tang, H., He, L., Fang, X., Zhao, J., Wang, X., Qi, Y., Sun, C., Lin, Y., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.17.255158 · Cited by 4
HieRFIT: Hierarchical Random Forest for Information TransferPreprint
Kaymaz, Y., Ganglberger, F., Tang, M., Fernández-Albert, F., Lawless, N., & Sackton, T. B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.16.300822 · Cited by 4
Concept Learners for Few-Shot LearningPreprint
Cao, K., Brbić, M., & Leskovec, J. (2020) · arXiv (Cornell University) · doi:10.48550/arxiv.2007.07375 · Cited by 52
Lung mesenchymal cell diversity rapidly increases at birth and is profoundly altered by hyperoxiaPreprint
Zanini, F., Che, X., Suresh, N. E., Knutsen, C., Klavina, P. A., Xie, Y., Domingo-Gonzalez, R., Liu, M., Jones, R. C., Quake, S. R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.19.444776 · Cited by 4
“Tagmentation and barcoding of cDNA was prepared using in-house Tn5 transposase and custom, double barcoded indices [21] .”
BackgroundMethodInfluentialMetabolic resilience is encoded in genome plasticityPreprint
Agudelo, L. Z., Tuyéras, R., Llinares, C., Morcuende, Á., Park, Y., Sun, N., Linna-Kuosmanen, S., Atabaki‐Pasdar, N., Ho, L., Galani, K., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-716965/v1 · Cited by 5
TAS-Seq: A Robust and Sensitive Amplification Method for Beads-based ScRNA-seqPreprint
Shichino, S., Ueha, S., Hashimoto, S., Ogawa, T., Aoki, H., Wu, B., Chen, C.-Y., Kitabatake, M., Ouji-Sageshima, N., Sawabata, N., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-799008/v1 · Cited by 4
Single-cell dissection of obesity-exercise axis in adipose-muscle tissuesPreprint
Yang, J., Vamvini, M. T., Nigro, P., Ho, L., Galani, K., Alvarez, M., Tanigawa, Y., Laakso, M., Agudelo, L. Z., Pajukanta, P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.22.469622 · Cited by 4
[New classification of endobronchial tuberculosis and balloon dilatation of bronchial stenosis].
Shim, Y.-S. (1992) · PubMed · Cited by 4
Patil, A. R., Schug, J., Naji, A., Kaestner, K. H., Faryabi, R. B., & Vahedi, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.03.522578 · Cited by 4
MuSK-BMP signaling in adult muscle stem cells maintains quiescence and regulates myofiber sizePreprint
Madigan, L. A., Jaime, D., Chen, I., & Fallon, J. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.17.541238 · Cited by 5
“This finding is in accord with snRNAseq studies showing MuSK transcript in quiescent SCs(Petrany et al., 2020; Shcherbina et al., 2020; Tabula Muris Consortium et al., 2018; Zeng et al., 2022).”
BackgroundResultMourad, O., Vohra, S., & Nunes, S. S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.03.547550 · Cited by 4
“Analysis of the Tabula Muris atlas (6) revealed that SLC5A2 was only detected in kidney epithelial cells, showing conserved expression patterns across species (Figure S1E).”
BackgroundHeterogeneity and Functional Analysis of Cardiac Fibroblasts in Heart DevelopmentPreprint
Deng, Y., He, Y., Xu, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.30.551164 · Cited by 4
Cober, N. D., McCourt, E. R., Godoy, R. S., Deng, Y., Schlosser, K., Situ, A., Cook, D. P., Lemay, S.-E. S., Klouda, T. M., Yuan, K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.06.555321 · Cited by 4
“Single-cell RNA sequencing (scRNA-seq) has been widely employed to better characterize lung cell populations under homeostatic conditions, 7,8 and in various disease states.”
MethodRGS2 is an innate immune checkpoint for TLR4 and Gαq-mediated IFNγ generation and lung injuryPreprint
Joshi, J. C., Joshi, B., Zhang, C., Banerjee, S., Vellingiri, V., Ragunathrao, V. A. B., Zhang, L., Amin, M. R., Song, Y., & Mehta, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.22.559016 · Cited by 4
“A prime example is RGS2, which can inhibit signaling mediated by Gq and, to a lesser extent, Gi and Gs protein (Ji et al., 2011; Klepac et al., 2019; Takimoto et al., 2009).”
BackgroundGarcía-Vicente, L., Borja, M., Tran, V., Álvarez-Vázquez, A., Flores-Hernández, R., Granados, A. A., McGeever, A., Kim, Y.-J., Dorman, L. C., Detweiler, A. M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.26.564166 · Cited by 4
Comprehensive analysis methods for developmental GC exposed zebrafish v3Preprint
Choi, M., Cook, A., Eachus, H., Tochwin, A., Kuntz, S., & Ryu, S. (2023) · doi:10.17504/protocols.io.kxygx9ooog8j/v3 · Cited by 4
Cheng, Z., Wei, S., Wang, Y., Wang, Y., Lu, Q. R., Wang, Y., & Yu, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.12.589306 · Cited by 3
Disentangling associations between complex traits and cell types with seismicPreprint
Lai, Q., Dannenfelser, R., Roussarie, J.-P., & Yao, V. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.04.592534 · Cited by 4
Wang, L., Liu, S., Zhang, S. X., et al. (2024) · eLife · doi:10.7554/elife.99790 · Cited by 4
NKX2.2 and KLF4 cooperate to regulate α-cell identityPreprint
Brooks, E. P., Casey, M. R., Wells, K. L., Liu, T.-Y., Orman, M. V., & Sussel, L. (2024) · Genes & Development · doi:10.1101/gad.352193.124 · Cited by 5
End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MSPreprint
Liu, Z., Dong, W., Gu, L., Ge, R., Zeng, X., Deng, J., Zhang, H., & Ye, Z. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.03.686420 · Cited by 3
“Existing single-cell transcriptomics dissociation methods 30-32 are insufficient for proteomics, as they prioritize RNA preservation without addressing protein-specific issues such as cellular debris interference.”
Computational challenges of cell cycle analysis using single cell transcriptomics
Chervov, A., & Zinovyev, A. (2022) · arXiv · doi:10.48550/arxiv.2208.05229 · Cited by 4
Ortiz, J., Ghazalli, N., Lopez, K., Rawson, J., McCown, E. M., Oh, E., Irimia, J. M., Jou, K., Mares, J., Chen, M.-H., et al. (2024) · Diabetes · doi:10.2337/db23-0490 · Cited by 3
Retinoid signaling in pancreas development, islet function, and disease
Bandral, M., Sussel, L., & Lorberbaum, D. S. (2024) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2024.10.007 · Cited by 4
scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss
Meng, H., Qin, C., & Long, Z. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf044 · Cited by 3
Discovering DISCO: application value of a large-scale repository for diverse single-cell omics data
Tao, W., Li, H., Zhang, J., Yin, Y., Fu, X., Chen, Y., Wang, Y., Zhou, Y., Gao, Z., Luo, H., et al. (2025) · Advanced technology in neuroscience . · doi:10.4103/atn.atn-d-24-00035 · Cited by 3
Winkler, M., Staniczek, T., Suhayda, M., Kürschner, S. W., Hoffmann, J., Cordero, J., Kraske, L., Maude, H., Nagy, D., Manco, R., et al. (2025) · JHEP Reports · doi:10.1016/j.jhepr.2025.101475 · Cited by 5
“27 Therefore, the role of endothelial Cxcl12 in liver fi bro-genesis requires further investigation.”
A single-cell atlas of the murine limb skeleton integrating the developmental and adult stages
Herpelinck, T., Ory, L., Verbraeken, T., Nasello, G., Barzegari, M., Bolander, J., Luyten, F. P., Tylżanowski, P., & Geris, L. (2025) · Scientific Reports · doi:10.1038/s41598-025-05277-6 · Cited by 15
Nutrient sensing in intestinal stem cell: Linking dietary nutrients to cellular metabolic regulation
Li, W., Yuan, X.-Y., Wang, Z., & Lin, R. (2025) · World Journal of Stem Cells · doi:10.4252/wjsc.v17.i7.107770 · Cited by 4
Single-nucleus profiling of Ossabaw pig atherosclerosis model
Bondareva, O., Hausner, M., Konert, M., Branzan, D., Noreikat, K., Oßmann, S., Sopromadze, L., Geisler, A. A., Heegaard, P. M. H., Sheikh, B. N., et al. (2025) · iScience · doi:10.1016/j.isci.2025.113464 · Cited by 3
GPRC5B preserves a mature β cell state in obesity by controlling MafA expression
Wang, T., Bonnavion, R., Piesker, J., Günther, S., & Wettschureck, N. (2025) · JCI Insight · doi:10.1172/jci.insight.194115 · Cited by 4
“JCI Insight 2025;10(20):e194115 https://doi.org/10.1172/jci.insight.194115 extrapancreatic cells such as neurons, fibroblasts, or smooth muscle cells (8, 9).”
InfluentialRXFP1, the relaxin receptor: Lost and found in translation
Lal, M., Eddy, S. F., Walentinsson, A., Hodgin, J. B., Hansen, P. B. L., Althage, M., & Kretzler, M. (2025) · Drug Discovery Today · doi:10.1016/j.drudis.2025.104483 · Cited by 3
Organoid Modeling of Mouse Anterior Tongue Epithelium Reveals Regional and Cellular Identities
Kim, S., Verweij, L. H. G., Lin, L., van Es, J. H., Slack, J. P., Winkel, C., Candelli, T., Lijnzaad, P., Margaritis, T., Breimer, G. E., et al. (2025) · Advanced Science · doi:10.1002/advs.202506738 · Cited by 4
Luxen, M., van der Aart, T. J., Jongman, R. M., Zwiers, P. J., Moser, J., Pultar, M., Skalicky, S., Diendorfer, A. B., Bouma, H. R., Koeze, J., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-17319-0 · Cited by 4
Liu, Z., Yang, Y., Song, L., Ruan, X., Li, X., He, Y., Zou, Y., Ding, S., & Sun, Y. (2025) · Journal of Innate Immunity · doi:10.1159/000548603 · Cited by 6
“Single-cell expression profile data of P2X1, P2X2, P2X3, P2X4, P2X5, P2X6, P2X7 in heart tissue were obtained from Tabula Muris (https://tabula-muris.ds. czbiohub.org/) [43].”
Duffy, F. J., Neal, M. L., Plumlee, C. R., Cohen, S. B., Gern, B. H., Diercks, A. H., Gerner, M. Y., Urdahl, K. B., & Aitchison, J. D. (2026) · PLoS Pathogens · doi:10.1371/journal.ppat.1013635 · Cited by 5
Deciphering splicing heterogeneity at single-cell resolution by SCSES
Xiao, W., Lv, X., Guo, D. H., Han, N., Zhou, L., Wang, P., & Liu, Z. (2025) · Nature Communications · doi:10.1038/s41467-025-64517-5 · Cited by 6
Integrative multi-omics analysis in vivo identifies influenza virus host factors
Shriver, L. P., Polacco, B. J., Eckhardt, M., Chang, M. W., Martínez‐Romero, C., Adkins-Travis, K., Cahalane, C., Haas, K. M., Stein, D. A., Fourati, S., et al. (2025) · iScience · doi:10.1016/j.isci.2025.113644 · Cited by 3
Basophils activate oncostatin M receptor–expressing vagal sensory neurons
Wang, J.-C., Park, K., Roger, A., Nikpoor, A. R., Crosson, T., Sunwoo, H. H., Kaufmann, E., Rafei, M., Chang, E. H., & Talbot, S. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.10.027 · Cited by 3
ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization
Sankarasubramanian, J., & Guda, C. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013721 · Cited by 3
Evolutionary dynamics of FoxQ2 transcription factors across metazoans reveals three ancient paralogs
Gattoni, G., Lin, C.-Y., York, J. R., Shew, C. J., Keitley, D., LaBonne, C., Yu, J.-K., Gillis, J. A., & Benito‐Gutiérrez, È. (2025) · Communications Biology · doi:10.1038/s42003-025-09368-y · Cited by 6
“The following amphioxus and vertebrate datasets were subsetted as describedandintegratedwithSAMapusingthedefaultpipeline 71 : B. fl oridae larval (T1) endoderm subset from original dataset 69 ; B. fl oridae adult gut tissues (batchB and control samplesonly) 70 ; D. rerio endoderm subset from original dataset (all develo…”
Bomfim, G. H. S., Asam, K. R., Patel, N., Zou, A., Rosenberg, K., Mitaishvili, E., Aguiar, T. F. M., Zorn, E., Ramasamy, R., Aouizerat, B., et al. (2026) · The Journal of Physiology · doi:10.1113/jp290475 · Cited by 4
Whole-organ and whole-body 3D atlases enable cellome-wide profiling
Yoshida, S. Y., Matsumoto, K., Takagi, S., Kinoshita, F. L., Yamashita, K., Shigeta, D., Yoshioka, Y., Ushiku, T., Morii, E., Susaki, E. A., et al. (2026) · Cell · doi:10.1016/j.cell.2025.12.057 · Cited by 6
Meldrum, K., Kosoko, A., & Leonard, M. (2026) · Particle and Fibre Toxicology · doi:10.1186/s12989-026-00675-8 · Cited by 3
“The specificity of interpolation gene sets for cell type was confirmed through comparison to AMP1, AMP2 and published ScSeq lung datasets [24, 25, 30, 35, 40] (Supplementary Figure S3A-B).”
Caspase 5c amplifies Wnt via APC cleavage to promote intestinal homeostasis
Jia, B., Shi, Y., Hong, Y., Yang, C., Roycroft, D., Kamal, S., Mukherjee, S., Ueberheide, B. M., Grier, A., Bank, J. L. C., et al. (2026) · Nature · doi:10.1038/s41586-026-10343-8 · Cited by 4
Atlas of lysosomal aging reveals a metabolite signature shared with lysosomal storage disorders
Puszynska, A. M., Nguyen, T. P., Cangelosi, A. L., Armani, A., Roberts, J. M., Singh, K. A., Cameron, J. C., Tseyang, T., Liu, G. Y., Lai, S., et al. (2026) · Science · doi:10.1126/science.ady0832 · Cited by 8
The Idd2 Locus Confers Prominent Resistance to Autoimmune Diabetes
Lombard‐Vadnais, F., Collin, R., Daudelin, J., Chabot‐Roy, G., Labrecque, N., & Lesage, S. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.2100456 · Cited by 3
RefTM: reference-guided topic modeling of single-cell chromatin accessibility data
Zhang, Z., Chen, S., & Lin, Z. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac540 · Cited by 3
HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data
Zhang, W., Cui, Y., Liu, B., Loza, M., Park, S., & Nakai, K. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae152 · Cited by 3
Characterization of dUTPase expression in mouse postnatal development and adult neurogenesis
Nagy, N. T., Hádinger, N., Tóth, O., Rácz, G. A., Pintér, T., Gál, Z., Urbán, M., Gócza, E., Hiripi, L., Acsády, L., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-63405-0 · Cited by 3
A single cell RNA sequence atlas of the early Drosophila larval eye
Raja, K. K. B., Yeung, K., Li, Y., et al. (2024) · BMC Genomics · doi:10.1186/s12864-024-10423-x · Cited by 3
“Single cell atlases have been generated from tissues of several model organisms, including mus musculus [4], Caenorhabditis elegans [5] and efforts to generate comprehensive whole-organism single cell atlases across development are underway to understand organismal development and biology.”
Guo, Q., Yuan, M., Zhang, L., & Deng, M. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae305 · Cited by 3
“The first dataset is a human lung dataset LungSS2 (SmartSeq2) [32] and the reference dataset we select is another human lung dataset Lung10X [32] sequenced from 10X Chromium platform.”
MethodYuan, L., Xu, Z., Li, Z., Zhang, S., Hu, C., Yu, W., Wei, H., Wang, X., & Geng, Y. (2024) · Lecture notes in computer science · doi:10.1007/978-981-97-5692-6_6 · Cited by 3
mitoXplorer 3.0, A Web Tool for Exploring Mitochondrial Dynamics in Single-cell RNA-seq Data
Haering, M., Bondio, A. D., Puccio, H. M., & Habermann, B. H. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169004 · Cited by 3
Cholinergic regulation of thymocyte negative selection
Liu, S., Zheng, C., Nechanitzky, R., Luo, P., Ramachandran, P., Nguyen, D., Elia, A., Jafari, S. M., Law, R., Snow, B. E., et al. (2025) · Nature Immunology · doi:10.1038/s41590-025-02152-4 · Cited by 6
“Therefore, ChAT expression Article https://doi.org/10.1038/s41590-025-02152-4 database 18 .”
InfluentialMulti-view clustering for single-cell RNA-seq data based on graph fusion
Wang, J., Xia, J., Tan, D., Ma, Y., Su, Y., & Zheng, C.-H. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf193 · Cited by 3
scGANSL: Graph Attention Network with Subspace Learning for scRNA-seq Data Clustering
Shu, Z., Ren, Y., Long, Q., Wang, H., & Yu, Z. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00731 · Cited by 3
Linking individual fitness to the evolution of cognition
Sheehan, M. J., & Miller, S. (2025) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2024.0122 · Cited by 3
scGT:integration algorithm for single-cell RNA-seq and ATAC-seq based on graph transformer
Qi, Y., Kan, Y., Qi, J., & Jin, S. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf357 · Cited by 6
“In contrast, there is a large number of well-annotated scRNA-seq datasets (Tabula Muris Consortium et al. 2018, Cao et al. 2020).”
Adil, A., Bhattacharya, N., Aadam, Khan, N. J., & Asger, M. (2025) · Scientific Reports · doi:10.1038/s41598-025-12897-5 · Cited by 4
“This dataset is part of the Tabula Muris Senis compendium, which profiles single-cell transcriptomes across 20 tissues from Mus musculus, comprising approximately 100,000 cells in total 23 .”
Choe, J., Belmonte, P. J., Crotts, S. B., Nguyen, T., Friedman, D. J., Zastrow, A. L., Rajcula, M. J., Hammer, B., Wilhelm, C., Shapiro, M. J., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci181207 · Cited by 3
“ST8Sia6 is not normally expressed in β cells (from Tabula Muris, Tabula Sapiens, or UCSC Cell Browser) (33–35).”
Chen, X., Cheng, J., Kong, L., Shu, X., Xu, H., Inoue, M., Fernández-Berrocal, M. S., Døskeland, D. S., Bjørås, M., Sivakumar, S., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03708-1 · Cited by 3
Bartz, J., Ma, X., Zhang, L. J., & Dong, X. (2025) · Communications Biology · doi:10.1038/s42003-025-08845-8 · Cited by 4
Wang, Y., & Zhao, H. (2026) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkag026 · Cited by 3
“Apart from tissue-specific data, we also collected a mouse atlas (Cusanovich et al. 2018; Tabula Muris Consortium et al. 2018) and a human fetal atlas dataset (Domcke et al. 2020; Cao et al. 2020a).”
gCAnno: a graph-based single cell type annotation method
Yang, X., Gao, S., Wang, T., et al. (2020) · BMC Genomics · doi:10.1186/s12864-020-07223-4 · Cited by 3
Yamagata, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23020613 · Cited by 3
“One precedent is the Tabula Muris project which created a compendium of singlecell transcriptome data from the experimental model organism Mus musculus comprising nearly 100,000 cells from 20 organs and tissues [88].”
BackgroundAI Knowledge Transfer from the University to Society
Martín, J. G., Lilić, M., & Martínez, M. R. (2022) · CRC Press eBooks · doi:10.1201/9781003276609 · Cited by 3
Telomerase Reverse Transcriptase Expression Marks a Population of Rare Adipose Tissue Stem Cells
Lynes, M. D., Carlone, D. L., Townsend, K. L., Breault, D. T., & Tseng, Y. (2022) · Stem Cells · doi:10.1093/stmcls/sxab005 · Cited by 5
Cell-Type Heterogeneity in DNA Methylation Studies: Statistical Methods and Guidelines
Teschendorff, A. E. (2022) · Springer eBooks · doi:10.1007/978-3-030-94475-9_4 · Cited by 2
Laise, P., Bosker, G., Califano, A., & Alvarez, M. J. (2022) · Current Protocols · doi:10.1002/cpz1.544 · Cited by 4
Muto, K., Tsuchiya, I., Kim, S. H., Nagasawa, S., Takishita, M. N., Tsugawa, K., Saito, H., Komazaki, Y., Torii, T., Fujii, T., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-19391-2 · Cited by 3
Antibodies as drugs—a Keystone Symposia report
Cable, J., Saphire, E. O., Hayday, A., Wiltshire, T. D., Mousa, J. J., Humphreys, D. P., Breij, E. C. W., Bruhns, P., Broketa, M., Furuya, G., et al. (2022) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14915 · Cited by 3
Edwards‐Faret, G., de Vin, F., Ślęzak, M., Gollenbeck, L., Karaman, R., Shinmyo, Y., Batiuk, M. Y., Menacho, C., Urschitz, J., Rincón, M. Y., et al. (2022) · Neuroscience · doi:10.1016/j.neuroscience.2022.11.029 · Cited by 3
“We based our experiments on the previously reported pmhyGENIE-3 system, which carries both an engineered self-inactivating piggyBac transposase and desired transgene cassette on a single plasmid (Urschitz et al., 2010).”
BackgroundMethodRetractedde Villarreal, J. M., Kalisz, M., Piedrafita, G., Graña‐Castro, O., Chondronasiou, D., Serrano, M., & Real, F. X. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac737 · Cited by 3
Dysregulation of polarity proteins in astrocyte reactivity
Luo, J. (2023) · Ageing Research Reviews · doi:10.1016/j.arr.2023.101869 · Cited by 3
Adipose tissue lymphatic endothelial cells: revisited functions in the modulation of adipose biology
AlZaim, I., Festa, J., & Kalucka, J. M. (2023) · Current Opinion in Physiology · doi:10.1016/j.cophys.2023.100675 · Cited by 5
Xie, J., Zhang, K., & Zhang, X. (2023) · Gynecology and Obstetrics Clinical Medicine · doi:10.1016/j.gocm.2023.04.005 · Cited by 3
Zhong, G., Choi, Y. A., & Shen, Y. (2023) · Communications Biology · doi:10.1038/s42003-023-05155-9 · Cited by 3
Leng, F., Mei, S., Zhou, X., Liu, X., Yuan, Y., Xu, W., Hao, C., Guo, R., Hao, C., Li, W., et al. (2023) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzad007 · Cited by 3
“Furthermore, leveraging single-cell transcriptomics data from similar tissues as a reference holds significant promise, given the extensive efforts of cell atlas consortia in generating massive amounts of single-cell transcriptomics data [32,33].”
scEVOLVE: cell-type incremental annotation without forgetting for single-cell RNA-seq data
Zhai, Y., Chen, L., & Deng, M. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae039 · Cited by 4
Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues
Nieuwenhuis, T. O., Giles, H. H., Arking, J. V. A., Patil, A. H., Shi, W., McCall, M. N., & Halushka, M. K. (2024) · Laboratory Investigation · doi:10.1016/j.labinv.2024.102069 · Cited by 5
Mansueto, A. J., & Good, D. J. (2024) · Journal of Molecular Evolution · doi:10.1007/s00239-024-10165-0 · Cited by 4
Wang, Z., Wang, W., Li, W., Yao, Y., Liu, W., & Tang, Z. (2024) · The Innovation Life · doi:10.59717/j.xinn-life.2024.100075 · Cited by 3
Palit, S., Shrestha, A. K., Thapa, S., Grimm, S. L., Coarfa, C., Theis, F., Simon, L. M., & Shivanna, B. (2024) · Genes · doi:10.3390/genes15060806 · Cited by 3
Netrin-1 Is an Important Mediator in Microglia Migration
Yu, H., Liu, X., Yin, Y., Liu, X.-N., Feng, Y.-Y., Tahir, M. M., Miao, X.-Z., He, X., He, Z., & Zhu, X. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25137079 · Cited by 3
Wang, H.-P., He, J. X., He, J., et al. (2024) · Inflammation Research · doi:10.1007/s00011-024-01951-z · Cited by 3
The syntaxin-binding protein STXBP5 regulates progerin expression
Qi, H., Wu, Y., Zhang, W., Yu, N., Lu, X., & Liu, J. (2024) · Scientific Reports · doi:10.1038/s41598-024-74621-z · Cited by 3
“6G. Analysis of the SASP pathway from the Reactome pathways databas releveled that the expression of CDK6, ANAPC1, EHMT1, UBA52, RPS27A and UBE2C was increased, although that of ANAPC7, UBB and ANAPC11 was not 33,37,38 (Fig.”
Metadata
- Authors
- The Tabula Muris Consortium, coordination, O., coordination, L., processing, O. C. A., sequencing, L. P. A., analysis, C. D., annotation, C. T., Writing group, Supplemental text writing group, & Principal investigators
- Venue
- Nature
- Published
- 2018-10
- Volume
- 562
- Issue
- 7727
- Pages
- 367-372
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6642641
- OpenAlex
- W2894687190
- Cited by
- 2,842
- References
- 32
- Citations by year
- 2026: 329 · 2025: 382 · 2024: 384 · 2023: 379 · 2022: 391 · 2021: 412 · 2020: 380 · 2019: 167 · 2018: 14
- FWCI
- 77.50
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Jagiellonian University Repository (Jagiellonian University) (submittedVersion, cc-by-nc-nd)
- eScholarship (California Digital Library) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- U.S. Department of Veterans Affairs (I01 BX002324, I01RX001222)
- National Institute on Aging (DP1AG053015, P01AG036695)
- National Heart, Lung, and Blood Institute (R00HL127267)
- National Cancer Institute (R01CA157877)
- National Institute on Deafness and Other Communication Disorders (R01DC016892)
- National Institute of Diabetes and Digestive and Kidney Diseases (K08DK101603, P30DK026743, P30DK116074)
- U.S. National Library of Medicine (DP1LM012179)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- Tabula Muris, mouse organs, single-cell transcriptomics, cell types, gene expression, cell atlas, T cells, endothelial cells, fluorescence-activated cell sorting, Mus musculus
- MeSH terms
- Animals, Cell Biology, Female, Flow Cytometry, Male, Mice, Inbred C57BL, Organ Specificity, T-Lymphocytes, Transcription Factors, Gene Expression Profiling, Endothelial Cells, Microfluidics, Mice, Single-Cell Analysis, Transcriptome
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 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
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
