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.
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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
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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.
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- 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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- 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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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- 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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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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.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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.
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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.
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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.
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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.
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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.
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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.
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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 1,701–1,800 of 2,952
Zheng, C., Wang, Y., Cheng, Y., Wang, X., Wei, H., King, I., & Li, Y. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae112 · Cited by 6
CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics
Zhao, Y., Kohl, C., Rosebrock, D., Hu, Q., Hu, Y., & Vingron, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae480 · Cited by 5
Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data
Tiong, K.-L., Luzhbin, D. A., & Yeang, C. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05825-3 · Cited by 6
“We downloaded the single-cell RNASeq data of the Tabula Muris database [45], selected 2690 cells from five cell types—oligodendrocytes, T cells, lung endothelial cells, hepatocytes, and fibroblast cells—and 643 marker genes which were differentially expressed in one cell type (see Sect.”
MethodInsulin and leptin oscillations license food-entrained browning and metabolic flexibility
Mattar, P., Reginato, A., Lavados, C., Das, D., Kalyani, M., Martínez-López, N., Sharma, M., Skovbjerg, G., Skytte, J. L., Roostalu, U., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114390 · Cited by 6
μ-Opioid receptor transcriptional variants in the murine forebrain and spinal cord
Chrószcz, M., Hajto, J., Misiołek, K., Szumiec, Ł., Ziemiańska, M., Radlicka-Borysewska, A., Borczyk, M., Zięba, M., Gołda, S., Siwiec, M., et al. (2024) · Gene · doi:10.1016/j.gene.2024.148890 · Cited by 6
Liver adrenoceptor alpha-1b plays a key role in energy and glucose homeostasis in female mice
Silva, A. J., Mouchiroud, M., Lavoie, O., Beji, S., Elmquist, J. K., & Caron, A. (2024) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00153.2024 · Cited by 6
Tissue‐specific functions of MSCs are linked to homeostatic muscle maintenance and alter with aging
Kurosawa, T., Ikemoto‐Uezumi, M., Yoshimoto, Y., Minato, K., Kaji, N., Chaen, T., Hase, E., Minamikawa, T., Yasui, T., Horiguchi, K., et al. (2024) · Aging Cell · doi:10.1111/acel.14299 · Cited by 7
“PDGFR α also marks MSC/fibroblast populations in various other organs (Tabula Muris Consortium, 2018).”
Kamizaki, K., Katsukawa, M., Yamamoto, A., Fukada, S., Uezumi, A., Endo, M., & Minami, Y. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-07173-9 · Cited by 7
Evaluation of the role of hepatic Gstm4 in diet-induced obesity and dyslipidemia
Hu, L., Yuan, D., Zhu, Q., et al. (2024) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2024.150920 · Cited by 6
Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data
Park, S., & Lee, H. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae586 · Cited by 5
Decoding SFRP2 progenitors in sustaining tooth growth at single-cell resolution
Zhao, T., Zhong, Q., Sun, Z., Yu, X., Sun, T., & An, Z. (2025) · Stem Cell Research & Therapy · doi:10.1186/s13287-025-04190-z · Cited by 6
Cardiac Nonmyocyte Subpopulations: A Secular Congregation
Sussman, M. A. (2019) · Regenerative Medicine · doi:10.2217/rme-2019-0053 · Cited by 6
Hao, X., Wang, K., Dai, C., Ding, Z., Yang, W., Wang, C., & Cheng, S. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa188 · Cited by 6
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
Maehara, K., Tomimatsu, K., Harada, A., Tanaka, K. Y., Sato, S., FUKUOKA, M., Okada, S., Handa, T., Kurumizaka, H., Saitoh, N., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110323 · Cited by 6
Xu, F., Guan, N., Xu, E., Ye, M., & Li, C. (2021) · Disease Markers · doi:10.1155/2021/8585633 · Cited by 6
Malhi, N. K., Luo, Y., Tang, X., Sriram, K., Calandrelli, R., Zhong, S., & Chen, Z. B. (2022) · Journal of Visualized Experiments · doi:10.3791/63307 · Cited by 7
Zhao, X., Chong, Z., Chen, Y., Zheng, X. L., Wang, Q., & Li, Y. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102517 · Cited by 7
MHC II – EGFP knock-in mouse model is a suitable tool for systems and quantitative immunology
Pačes, J., Knížková, K., Tušková, L., Grobárová, V., Zadražil, Z., Boes, M. L., & Černý, J. (2022) · Immunology Letters · doi:10.1016/j.imlet.2022.10.007 · Cited by 5
TRAIL inhibition by soluble death receptor 5 protects against acute myocardial infarction in rats
Wang, M., Wei, Y., Wang, X., et al. (2022) · Heart and Vessels · doi:10.1007/s00380-022-02197-7 · Cited by 6
SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data
Gan, D., & Li, J. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac819 · Cited by 6
The RNA-Seq data analysis shows how the ontogenesis defines aging
Salnikov, L., Goldberg, S. I., Rijhwani, H., Shi, Y., & Pinsky, E. (2023) · Frontiers in Aging · doi:10.3389/fragi.2023.1143334 · Cited by 6
Single-cell RNA sequencing of mouse lower respiratory tract epithelial cells: A meta-analysis
Martins, L. R., Glimm, H., & Scholl, C. (2023) · Cells and Development · doi:10.1016/j.cdev.2023.203847 · Cited by 8
Emfinger, C. H., Clark, L. E., Yandell, B. S., Schueler, K. L., Simonett, S. P., Stapleton, D. S., Mitok, K. A., Merrins, M. J., Keller, M. P., & Attie, A. (2023) · eLife · doi:10.7554/elife.88189 · Cited by 7
Unique miRNome and transcriptome profiles underlie microvascular heterogeneity in mouse kidney
Luxen, M., Zwiers, P. J., Meester, F., et al. (2023) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00005.2023 · Cited by 6
SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data
Tzaferis, C., Karatzas, E., Baltoumas, F. A., Pavlopoulos, G. A., Kollias, G. A., & Konstantopoulos, D. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.10.032 · Cited by 9
“…for example, has played a crucial role in the comprehensive annotation of cell types in multiple organisms (e.g., Human Cell Atlas for Homo sapiens [12], Tabula Muris for Mus musculus [13]), as well as in the identification of novel cell populations, sub-populations and disease states [14].”
BackgroundHuman-Spa: An Online Platform Based on Spatial Transcriptome Data for Diseases of Human Systems
Su, Y., Yan, S., Cao, C., et al. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385302 · Cited by 6
Embigin deficiency leads to delayed embryonic lung development and high neonatal mortality in mice
Talvi, S., Jokinen, J., Sipilä, K. H., Rappu, P., Zhang, F., POUTANEN, M. H., Rantakari, P., & Heino, J. (2024) · iScience · doi:10.1016/j.isci.2024.108914 · Cited by 6
Advances and challenges in investigating B-cells via single-cell transcriptomics
Skinner, O. P., Asad, S., & Haque, A. (2024) · Current Opinion in Immunology · doi:10.1016/j.coi.2024.102443 · Cited by 6
Embracing the informative missingness and silent gene in analyzing biologically diverse samples
Du, D., Bhardwaj, S., Lu, Y., Wang, Y., Parker, S. J., Zhang, Z., Eyk, J. E. V., Yu, G., Clarke, R. C., Herrington, D. M., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-78076-0 · Cited by 6
An oxide transport chain essential for balanced insulin action
Wu, X., Chen, K., & Williams, K. J. (2020) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2020.02.006 · Cited by 5
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
Seirup, M., Chu, L., Sengupta, S., Leng, N., Browder, H., Kapadia, K., Shafer, C. M., Duffin, B. M., Elwell, A. L., Bolin, J. M., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0239711 · Cited by 6
Petrilli, L. L., Riccio, F., Giuliani, G., Palma, A., Gargioli, C., Vumbaca, S., Faron, M., Palmieri, G., Pasquini, L., Sacco, F., et al. (2021) · Journal of Clinical Medicine · doi:10.3390/jcm10040823 · Cited by 6
Spatial transcriptomics for respiratory research and medicine
Curras-Alonso, S., Soulier, J., Walter, T., Mueller, F., Londoño‐Vallejo, A., & Fouillade, C. (2021) · European Respiratory Journal · doi:10.1183/13993003.04314-2020 · Cited by 7
Elangovan, M., Ka, J., Pak, B., Choi, W., Oh, S., Jin, S., & Yoo, Y. J. (2021) · The FASEB Journal · doi:10.1096/fj.202100808rrr · Cited by 6
Recent Progress in Cardiovascular Research Involving Single-Cell Omics Approaches
Dai, Z., & Nomura, S. (2021) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2021.783398 · Cited by 7
“reexplored the scRNA-seq data from tissue-specific ECs in the Tabula Muris (4) and demonstrated that cardiac ECs could be classified as a separate cluster, even though they had considerable transcriptomic overlap with ECs from other tissues (47).”
MethodDecrypting the cellular and molecular intricacies associated with COVID-19-induced chronic pain
Rani, M., Uniyal, A., Akhilesh, A., & Tiwari, V. (2022) · Metabolic Brain Disease · doi:10.1007/s11011-022-01048-8 · Cited by 6
cKBET: assessing goodness of batch effect correction for single-cell RNA-seq
Zhao, Y., Guo, Y. B., & Li, L. (2023) · Frontiers of Computer Science · doi:10.1007/s11704-022-2111-8 · Cited by 6
Li, Q., Lin, J., Rosen, S. M., Zhang, T., Kazerounian, S., Luo, S., & Agrawal, P. B. (2020) · American Journal Of Pathology · doi:10.1016/j.ajpath.2020.08.012 · Cited by 6
Orchard, P., Manickam, N., Varshney, A., Rai, V., Kaplan, J. B., Lalancette, C., Gallagher, K. A., Burant, C., & Parker, S. C. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.01.183004 · Cited by 6
Single-cell identity definition using random forests and recursive feature eliminationPreprint
Park, M., Vorperian, S. K., Wang, S., & Pisco, A. O. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.03.233650 · Cited by 6
“The dataset’s deep 63 characterization of phenotype and physiology allowed us to explore TF reprogramming 64 protocols [14], as well as aging signatures [15], on the scale of hundreds of thousands of 65 cells.”
Atp13a5 Marker Reveals Pericytes of The Central Nervous System in MicePreprint
Guo, X., Ge, T., Xia, S., Wu, H., Colt, M., Xie, X., Zhang, B., Zeng, J., Chen, J., Zhu, D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.09.451694 · Cited by 6
Zaidi, S., Zhao, J. L., Chan, J. M., Roudier, M. P., Wadosky, K. M., Gopalan, A., Karthaus, W. R., Choi, J., Lawrence, K. E., Chaudhary, O., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.01.466599 · Cited by 6
Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomicsPreprint
Subramanian, A., Alperovich, M., Yang, Y., & Li, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.27.466176 · Cited by 6
Fragemann, J., Ardizzone, L., Egger, J., Kleesiek, J., & Workshop, M. (2022) · doi:10.36227/techrxiv.19364897.v1 · Cited by 6
Golf, S. R., Trotter, J. H., Wang, J., Nakahara, G., Han, X., Wernig, M., & Südhof, T. C. (2023) · eLife · doi:10.1101/2023.04.10.536254 · Cited by 8
CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactionsPreprint
Li, E., Benitez, C., Boggess, S. C., Koontz, M., Rose, I. V. L., Martinez, D., Dräger, N. M., Teter, O. M., Samelson, A. J., Pierce, N., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.26.538498 · Cited by 6
Cell segmentation and gene imputation for imaging-based spatial transcriptomicsPreprint
Zhong, Y., & Ren, X. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.26.564185 · Cited by 6
Activated Interferon Signaling Suppresses Age-Dependent Liver CancerPreprint
Havas, A. P., Lande, K., Rajesh, A., Evensen, K. G., Varanasi, S. K., Shang, L., Schmidt, E. K., Lee, J., Kim, K. H., Teneche, M. G., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.31.606057 · Cited by 6
Spanos, M., Gokulnath, P., Li, G., Hutchins, E. D., Meechoovet, B., Sheng, Q., Chatterjee, E., Sharma, R., Carnel-Amar, N., Lin, C., et al. (2024) · medRxiv · doi:10.1101/2024.09.19.24314009 · Cited by 7
Mouse Single-Cell Long-Read Splicing Atlas by Ouro-SeqPreprint
An, H., Choi, S. Y., Yi, J., Lim, C., Shin, S.-I., Oh, S., Lee, R. H., & Park, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.17.633678 · Cited by 6
Xu, C., Li, S., Cai, Y., Lu, J., Teng, Y., Yang, X. Y., & Wang, J. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25094666 · Cited by 6
“Here, to select candidate markers of cerebrovascular ECs, we screened several publicly available single-cell RNA-seq (scRNAseq) databases [10,11] and particularly focused on transporters.”
BackgroundIntegration of unpaired single cell omics data by deep transfer graph convolutional network
Kan, Y., Qi, Y., Zhang, Z., Liang, X., Wang, W., & Jin, S. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012625 · Cited by 7
Zhang, T., Zhao, Z., Ren, J., Zhang, Z., Zhang, H., & Wang, G. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf071 · Cited by 7
Tchouto, M. N., Bucher, C. H., Meß, A.-K., Haas, S. F., Schmidt‐Bleek, K., Duda, G. N., Beule, D., & Milek, M. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1511902 · Cited by 5
Ciccimarra, R., Zoboli, M., Ragionieri, L., Cacchioli, A., Gazza, F., Saleri, R., Stellari, F. F., & Ravanetti, F. (2025) · Annals of Anatomy - Anatomischer Anzeiger · doi:10.1016/j.aanat.2025.152660 · Cited by 6
Wang, J., Groennebaek, T., Nielsen, R. R., Pryds, K., de Paoli, F. V., Bøtker, H. E., & Vissing, K. (2025) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00275.2025 · Cited by 5
Byerly, K., Wolfe, C., Parris, H. J., Griggs, C., Wilson, E., Huff, M. L., Griggs, M., Morningstar, J. E., Guo, L., Tang, F., et al. (2025) · Cells · doi:10.3390/cells14110774 · Cited by 5
Li, Y., Torok, J., Zhang, S., Ding, J. L., Wang, N., Lau, C., Kulkarni, S., Anand, C., Tran, J., Cheng, M., et al. (2025) · Advanced Science · doi:10.1002/advs.202413052 · Cited by 5
A Flexible Data-Driven Framework for Correcting Coarsely Annotated scRNA-seq Data
Zheng, R., He, Y., Huang, J., Kan, S., Wang, H., Wang, E., & Li, M. (2025) · Big Data Mining and Analytics · doi:10.26599/bdma.2025.9020009 · Cited by 6
Zeissler, D., Busch, M., Grieskamp, S., et al. (2025) · Circulation · doi:10.1161/circulationaha.124.070236 · Cited by 5
Zhang, Y., Ming, W., Yu, B., Wang, L., Lu, K., Xu, L., Ni, Y., Deng, R., & Chen, D. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101105 · Cited by 6
Flow matching meets biology and life science: a survey
Li, Z., Zeng, Z., Lin, X., Fang, F., Qu, Y., Xu, Z., Liu, Z., Ning, X., Wei, T., Liu, G., et al. (2026) · npj Artificial Intelligence · doi:10.1038/s44387-025-00066-y · Cited by 21
Hyperglutaminolysis drives senescence and aging through arginine-mTORC1 axis activation
Chen, H., Huang, N., Xu, W., Yang, Y., Wang, F., Gong, H., Zhou, J., Tai, H., Zhao, T., Zhang, J., et al. (2026) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-026-02576-w · Cited by 6
“40,41 Our data revealed an upregulation of GLS1 protein levels and an increase in overall GLS activity in senescent cells (Fig.”
Hirdaramani, A., Cheng, C., Hanyaloglu, A. C., & Frost, G. S. (2026) · Communications Biology · doi:10.1038/s42003-026-09830-5 · Cited by 6
“Single-cell RNA-seq data from the Tabula Muris Project, generated by FACS-based full-length transcript analysis, were downloaded from the Gene Expression Omnibus (Table S1) 39 .”
Structural basis of liver de-targeting and neuronal tropism of CNS-targeted AAV capsids
Brittain, T. J., Jang, S., Coughlin, G. M., Hoang, J. D., Barcelona, B. H., Giriat, I., Ristic, F., Appling, N., Chossis, C. P., Shay, T. F., et al. (2026) · Molecular Therapy · doi:10.1016/j.ymthe.2026.03.030 · Cited by 7
“Unlike CAP-B10, these vectors target the CNS through the LRP6 receptor which, unlike LY6A, is also expressed in the liver 34,35,42–44 , where it contributes to vector transduction 45 .”
E96V Mutation in the Kdelr3 Gene Is Associated with Type 2 Diabetes Susceptibility in Obese NZO Mice
Altenhofen, D., Khuong, J. M.-A., Kuhn, T., Lebek, S., Görigk, S., Kaiser, K., Binsch, C., Grieß, K., Knebel, B., Belgardt, B., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24010845 · Cited by 5
Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census
Ghaddar, B., & De, S. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad714 · Cited by 6
“…lung (Kim et al. 2020, Wu et al. 2021a), and pancreas (Peng et al. 2019, Hwang et al. 2022) cancers, normal lung (Travaglini et al. 2020), colon (Smillie et al. 2019), and heart (Litvi (cid:2) nukova´ et al. 2020) datasets, and tissues from the Tabula Muris (Schaum et al. 2018) where applicable.”
BackgroundInfluentialHu, Y., Sun, Y., Li, T., Han, W., & Wang, P. (2023) · Genomics · doi:10.1016/j.ygeno.2023.110774 · Cited by 5
Transcription factor PBX4 regulates limb development and haematopoiesis in mice
Ning, Y., Duo, S., Lin, X., Zhang, H., Fei, J., Zhang, B., Zeng, Y., Xie, D., Chen, J., Liu, X., et al. (2024) · Cell Proliferation · doi:10.1111/cpr.13580 · Cited by 4
Tonic TCR and IL-1β signaling mediate phenotypic alterations of naive CD4+ T cells
Sekiya, T., Hidano, S., & Τακακι, S. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113954 · Cited by 5
Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms
Malekpour, S. A., Haghverdi, L., & Sadeghi, M. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae180 · Cited by 7
Rbm24 modulates neuronal RNA splicing to restrict cognitive dysfunction
Yao, D., Wang, X., Liu, J., & Xu, X. Q. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.133853 · Cited by 6
Hepatic lipopolysaccharide binding protein partially uncouples inflammation from fibrosis in MAFLD
Wang, D., Baghoomian, A., Zhang, Z., Cui, Y., Whang, E. C., Li, X., Fraga, J., Spellman, R. A., Dong, T. S., Li, W., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci179752 · Cited by 5
Prion diseases disrupt glutamate/glutamine metabolism in skeletal muscle
Caredio, D., Koderman, M., Frontzek, K. J., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012552 · Cited by 5
Lack of SMARCB1 expression characterizes a subset of human and murine peripheral T-cell lymphomas
Fischer, A., Albert, T., Moreno, N., Interlandi, M., Mormann, J., Glaser, S., Patil, P., de Faria, F. W., Richter, M., Verma, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52826-0 · Cited by 6
Tang, H., Zhong, J.-Y., Yu, X., Chai, H., Liu, R., & Zeng, T. (2024) · iScience · doi:10.1016/j.isci.2024.111131 · Cited by 5
Ranard, K. M., & Appel, B. (2024) · Journal of Lipid Research · doi:10.1016/j.jlr.2024.100716 · Cited by 6
CDK14 regulates the development and repair of lung
Chen, J., Wang, Y., Gao, R., Ma, L.-Y., Zhong, J., Yang, J., Deng, Z., Li, Y.-Y., Li, X., Shu, Y.-H., et al. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02292-4 · Cited by 5
LaRocca, T. J., & Lark, D. S. (2025) · Function · doi:10.1093/function/zqaf005 · Cited by 6
“…gener ated a tr anscriptomic map of 67 genes with esta b lished r oles in EV biogenesis, cargo sorting, secretion, and car go , 5 , 6 using data from the Tabula Muris , 7 —a public single-cell RNA-Seq dataset consisting of 44 779 cells from 117 cell populations found in 20 different mouse tissues.”
Kang, J., Li, Q., Liu, J., Du, L., Liu, P., Liu, F., Wang, Y., Shen, X., Luo, X., Wang, N., et al. (2025) · GigaScience · doi:10.1093/gigascience/giaf012 · Cited by 5
Association and shared biological bases between birth weight and cortical structure
Zhang, L., Ge, Q., Sun, Z., Zhang, R., Li, X., Luo, X., Tian, R., Cao, Y., Pu, C., Lin, L., et al. (2025) · Translational Psychiatry · doi:10.1038/s41398-025-03294-7 · Cited by 6
“Firstly, we used the Tabula Muris dataset, which contains 115 cell types from 18 mouse organs, of which 7 cell types are related to brain [37].”
Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering
Yu, X., Ren, Y., Xia, M., Shu, Z., & Zhu, L. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf198 · Cited by 7
Neuroendocrine cells orchestrate regeneration through Desert hedgehog signaling
Kong, W. W., Lu, W.-J., Dubey, M., Suryawanshi, R. K., Vijayakumar, S., Jeong, Y., Gombar, S., Diehn, M., Shin, K., Ott, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.05.012 · Cited by 5
A comparative study of manifold learning methods for scRNA-seq with a trajectory-aware metric
Nadjafikhah, M., & Nasiri, M. (2025) · Scientific Reports · doi:10.1038/s41598-025-14301-8 · Cited by 9
“• BAT (Brown Adipose Tissue), part of the Tabula Muris Senis FACS dataset 13 , hosted on Figshare by Angela Oliveira Pisco.”
Ye, X., Dong, Y., Han, J., et al. (2025) · International Immunopharmacology · doi:10.1016/j.intimp.2025.115459 · Cited by 5
Molecular analysis of vascular gene expression
van der Ent, M. A., Svilar, D., & Cleuren, A. C. A. (2022) · Research and Practice in Thrombosis and Haemostasis · doi:10.1002/rth2.12718 · Cited by 5
Applications of single‐cell multi‐omics sequencing in deep understanding of brain diseases
Zhang, X., Lü, P., & Shen, X. (2022) · Clinical and Translational Discovery · doi:10.1002/ctd2.95 · Cited by 6
Novel aspects of intra-islet communication: Primary cilia and filopodia
Moruzzi, N., Leibiger, B., Barker, C. J., Leibiger, I. B., & Berggren, P. (2022) · Advances in Biological Regulation · doi:10.1016/j.jbior.2022.100919 · Cited by 5
TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
Melzer, M. K., Schirge, S., Gout, J., Arnold, F., Srinivasan, D., Burtscher, I., Allgöwer, C., Mulaw, M., Zengerling, F., Günes, C., et al. (2023) · BMC Biology · doi:10.1186/s12915-023-01553-x · Cited by 5
Deosthale, P. J., Balanta‐Melo, J., Creecy, A., Liu, C., Marcial, A., Morales, L., Cridlin, J., Robertson, S., Okpara, C., Sanchez, D. J., et al. (2023) · Bone Research · doi:10.1038/s41413-023-00256-x · Cited by 5
“41 Of note, this study did not investigate the bone tissue transcriptome.”
A Multimodal Omics Framework to Empower Target Discovery for Cardiovascular Regeneration
Li, Z., Brittan, M., & Mills, N. L. (2023) · Cardiovascular Drugs and Therapy · doi:10.1007/s10557-023-07484-7 · Cited by 7
“Researchers have started building large-scale multi-organ single-cell transcriptomic atlases for different species such as Tabula Sapiens [22] and Tabula Muris [23] at an unprecedented speed.”
BackgroundGranados, A. A., Bucher, S., Agrawal, A., Song, H., Chen, A. T., Peng, T., Neff, N. F., Pisco, A. O., Huang, F. W., & Wang, B. (2023) · eLife · doi:10.7554/elife.81090 · Cited by 6
“We have previously shown that multi-organ, single-cell transcriptome-based approaches can yield significant insights into organ biology and cross-organ signaling ( Tabula Muris Consortium et al., 2018 ; Jones et al., 2022 ).”
BackgroundScreening single-cell trajectories via continuity assessments for cell transition potential
Zheng, Z., Chang, L., Li, Y., Liu, K., Mu, J., Zhang, S., Li, J., Wu, Y., Zou, L., Ni, Q., et al. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad356 · Cited by 7
Price, T. R., Emfinger, C. H., Schueler, K. L., King, S. M., Nicholson, R. J., Beck, T., Yandell, B. S., Summers, S. A., Holland, W. L., Krauss, R. M., et al. (2023) · Journal of Lipid Research · doi:10.1016/j.jlr.2023.100471 · Cited by 5
“The lack of genetic association in humans may be due to species differences where mice express Apobec1 in both liver and intestine (45), whereas human expression is restricted to the intestine (https://gtexportal.org/home/).”
BackgroundCharacterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses
Liu, D., Fu, Y., Wang, X., Wang, X., Fang, X., Zhou, Y., Wang, R., Zhang, P., Jiang, M., Jia, D., et al. (2023) · Stem Cell Reports · doi:10.1016/j.stemcr.2023.10.018 · Cited by 5
Transcriptomic-based roadmap to the healthy and ozone-exposed lung
Moos, P. J., Cheminant, J. R., Adhikari, U., & Venosa, A. (2023) · Current Opinion in Toxicology · doi:10.1016/j.cotox.2023.100445 · Cited by 5
Inoue, O., Goten, C., Hashimuko, D., Yamaguchi, K., Takeda, Y., Nomura, A., Ootsuji, H., Takashima, S., Iino, K., Takemura, H., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101337 · Cited by 5
Convergent differentiation of multiciliated cells
Chae, S., Park, T. J., & Kwon, T. (2023) · Scientific Reports · doi:10.1038/s41598-023-50077-5 · Cited by 5
Identification of ANKRD13D as a potential target in renal cell carcinomas
Zhou, W., Huang, Y., Liu, J., Liu, Y., Liu, Y., & Yu, C. (2024) · The International Journal of Biological Markers · doi:10.1177/03936155241236498 · Cited by 5
Mao, J., Bao, Y., Liu, F., Ye, Q., Peng, J., Nie, J., Huang, L., Liao, Y., Xing, Y., Wu, D., et al. (2024) · Journal of Neuroinflammation · doi:10.1186/s12974-024-03299-x · Cited by 7
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
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