Identification of a regeneration-organizing cell in the Xenopus tail
Open accessAbstract
A tale of tadpole tail regeneration: Some vertebrates, including some amphibians, show a remarkable, if sometimes restricted, ability to regenerate lost appendages. Aztekin et al. compared naturally occurring regeneration-competent and -incompetent Xenopus laevis tadpoles using single-cell messenger RNA sequencing. They identified regeneration-organizing cells (ROCs) that could coordinate tail regeneration. Relocation of ROCs from the body to the amputation plane enabled specialized wound epidermis formation and subsequent regeneration. ROCs simultaneously expressed many different ligands that can induce proliferation of different progenitor cell populations. Thus, by signaling to underlying progenitors, ROCs orchestrate the growth of a new appendage. Science , this issue p. 653
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
Within the compendium, fourteen studies had control groups that included six or more samples.
“Within our compendium, we identified a total of fourteen studies with control groups that included six or more samples5,6,15,49–59.”
From Confronting false discoveries in single-cell differential expression (2021) · cites this paper as [53]
The study description (section labeled Abstract; page not provided) reports uninjured, intact-tail samples alongside amputated-tail samples, supporting its identification as a study with a control condition. It says there were at least two biological replicates per condition, but does not establish that the control group had six or more samples. The count of fourteen studies is the citing authors’ compendium count, not a finding attributed to this individual source. (LLM, conf=0.77)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., & Satija, R. (2018) · Nature Biotechnology · doi:10.1038/nbt.4096 · Cited by 13,174 · see citing works
UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · see citing works
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
McInnes, L., Healy, J., & Melville, J. (2018) · arXiv · doi:10.48550/arxiv.1802.03426 · Cited by 7,101 · see citing works
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520 · see citing works
Dimensionality reduction for visualizing single-cell data using UMAP
Becht, E., McInnes, L., Healy, J., Dutertre, C.-A., Kwok, I. W. H., Ng, L. G., Ginhoux, F., & Newell, E. W. (2019) · Nature Biotechnology · doi:10.1038/nbt.4314 · Cited by 5,358 · see citing works
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944 · see citing works
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Lun, A. T. L., McCarthy, D. J., & Marioni, J. C. (2016) · F1000Research · doi:10.12688/f1000research.9501.2 · Cited by 1,586 · see citing works
Self-citationA step-by-step workflow for low-level analysis of single-cell RNA-seq data
Lun, A. T. L., McCarthy, D. J., & Marioni, J. C. (2016) · F1000Research · doi:10.12688/f1000research.9501.1 · Cited by 1,511 · see citing works
Self-citationGenome evolution in the allotetraploid frog Xenopus laevis
Session, A. M., Uno, Y., Kwon, T., Chapman, J. A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., et al. (2016) · Nature · doi:10.1038/nature19840 · Cited by 949 · see citing works
A draft network of ligand–receptor-mediated multicellular signalling in human
Ramilowski, J. A., Goldberg, T., Harshbarger, J., Kloppmann, E., Lizio, M., Satagopam, V. P., Itoh, M., Kawaji, H., Carninci, P., Rost, B., et al. (2015) · Nature Communications · doi:10.1038/ncomms8866 · Cited by 887 · see citing works
Classification of low quality cells from single-cell RNA-seq data
Ilicic, T., Kim, J. K., Kolodziejczyk, A. A., Bagger, F. O., McCarthy, D. J., Marioni, J. C., & Teichmann, S. A. (2016) · Genome Biology · doi:10.1186/s13059-016-0888-1 · Cited by 693 · see citing works
Self-citationConditional targeted cell ablation in zebrafish: A new tool for regeneration studies
Curado, S., Anderson, R. M., Jungblut, B., Mumm, J. S., Schroeter, E. H., & Stainier, D. Y. R. (2007) · Developmental Dynamics · doi:10.1002/dvdy.21100 · Cited by 509 · see citing works
Love, N. R., Chen, Y., Ishibashi, S., Kritsiligkou, P., Lea, R., Koh, Y. W. H., Gallop, J. L., Dorey, K., & Amaya, E. (2013) · Nature Cell Biology · doi:10.1038/ncb2659 · Cited by 486 · see citing works
Modulation of tissue repair by regeneration enhancer elements
Kang, J., Hu, J., Karra, R., Dickson, A. L., Tornini, V. A., Nachtrab, G. T., Gemberling, M. P., Goldman, J., Black, B. L., & Poss, K. D. (2016) · Nature · doi:10.1038/nature17644 · Cited by 315 · see citing works
Advances in signaling in vertebrate regeneration as a prelude to regenerative medicinePreprint
Stoick-Cooper, C. L., Moon, R. T., & Weidinger, G. (2007) · Genes & Development · doi:10.1101/gad.1540507 · Cited by 304 · see citing works
Molecular Pathways Needed for Regeneration of Spinal Cord and Muscle in a Vertebrate
Beck, C. W., Christen, B., & Slack, J. M. W. (2003) · Developmental Cell · doi:10.1016/s1534-5807(03)00233-8 · Cited by 284 · see citing works
The Molecular and Cellular Choreography of Appendage Regeneration
Tanaka, E. M. (2016) · Cell · doi:10.1016/j.cell.2016.05.038 · Cited by 234 · see citing works
Cell lineage tracing duringXenopustail regeneration
Gargioli, C., & Slack, J. M. W. (2004) · Development · doi:10.1242/dev.01155 · Cited by 198 · see citing works
Limb development: a paradigm of gene regulation
Petit, F., Sears, K. E., & Ahituv, N. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.167 · Cited by 188 · see citing works
Testing for differential abundance in mass cytometry data
Lun, A. T. L., Richard, A. C., & Marioni, J. C. (2017) · Nature Methods · doi:10.1038/nmeth.4295 · Cited by 181 · see citing works
Self-citationChen, J., Wang, Z., Zheng, Z., Chen, Y., Khor, S., Shi, K., He, Z., Wang, Q., Zhao, Y., Zhang, H., et al. (2017) · Cell Death and Disease · doi:10.1038/cddis.2017.490 · Cited by 176 · see citing works
Kawakami, Y., Esteban, C. R., Matsui, T., Rodríguez-León, J., Kato, S., & Belmonte, J. C. (2004) · Development · doi:10.1242/dev.01331 · Cited by 172 · see citing works
Requirement for Wnt and FGF signaling in Xenopus tadpole tail regeneration
Lin, G., & Slack, J. M. W. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.01.032 · Cited by 165 · see citing works
BMP signaling induces digit regeneration in neonatal mice
Yu, L., Han, M., Yan, M., Lee, E.-C., Lee, J., & Muneoka, K. (2010) · Development · doi:10.1242/dev.042424 · Cited by 145 · see citing works
Pandey, S., Shekhar, K., Regev, A., & Schier, A. F. (2018) · Current Biology · doi:10.1016/j.cub.2018.02.040 · Cited by 144 · see citing works
High-throughput transgenesis in Xenopus using I-SceI meganuclease
Ogino, H., McConnell, W. B., & Grainger, R. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.208 · Cited by 129 · see citing works
Beck, C. W., Christen, B., Barker, D. M., et al. (2006) · Mechanisms of Development · doi:10.1016/j.mod.2006.07.001 · Cited by 126 · see citing works
TGF-β signaling is required for multiple processes during Xenopus tail regeneration
Ho, D. M., & Whitman, M. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2007.12.031 · Cited by 106 · see citing works
Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration
Love, N. R., Chen, Y., Bonev, B., Gilchrist, M. J., Fairclough, L., Lea, R., Mohun, T. J., Paredes, R., Zeef, L. A. H., & Amaya, E. (2011) · BMC Developmental Biology · doi:10.1186/1471-213x-11-70 · Cited by 90 · see citing works
Early redox activities modulate Xenopus tail regeneration
Ferreira, F., Raghunathan, V. K., Luxardi, G., Zhu, K., & Zhao, M. (2018) · Nature Communications · doi:10.1038/s41467-018-06614-2 · Cited by 78 · see citing works
Imparting regenerative capacity to limbs by progenitor cell transplantation
Lin, G., Chen, Y., & Slack, J. (2012) · Developmental Cell · doi:10.1016/j.devcel.2012.11.017 · Cited by 76 · see citing works
Kostakopoulou, K., Vogel, A., Brickell, P. M., & Tickle, C. A. (1996) · Mechanisms of Development · doi:10.1016/0925-4773(95)00492-0 · Cited by 70 · see citing works
Tran, H. T., Sekkali, B., Imschoot, G. V., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1007725107 · Cited by 69 · see citing works
Early bioelectric activities mediate redox-modulated regeneration
Ferreira, F., Luxardi, G., Reid, B., & Zhao, M. (2016) · Development · doi:10.1242/dev.142034 · Cited by 63 · see citing works
pTransgenesis: a cross-species, modular transgenesis resource
Love, N. R., Thuret, R., Chen, Y., et al. (2011) · Development · doi:10.1242/dev.066498 · Cited by 61 · see citing works
Macroarray‐based analysis of tail regeneration in Xenopus laevis larvae
Tazaki, A., Kitayama, A., Terasaka, C., et al. (2005) · Developmental Dynamics · doi:10.1002/dvdy.20472 · Cited by 44 · see citing works
Spinal cord is required for proper regeneration of the tail in Xenopus tadpoles
Taniguchi, Y., Sugiura, T., Tazaki, A., Watanabe, K., & Mochii, M. (2008) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2007.00981.x · Cited by 43 · see citing works
Sugiura, T., Tazaki, A., Ueno, N., Watanabe, K., & Mochii, M. (2008) · Mechanisms of Development · doi:10.1016/j.mod.2008.10.002 · Cited by 43 · see citing works
Chen, C., & Poss, K. D. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024554 · Cited by 40 · see citing works
Li, J., Zhang, S., & Amaya, E. (2016) · Regeneration · doi:10.1002/reg2.69 · Cited by 37 · see citing works
Luna, R. I. M., & Zuber, M. E. (2018) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot100974 · Cited by 12 · see citing works
(2012) · Methods in molecular biology · doi:10.1007/978-1-61779-992-1 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Confronting false discoveries in single-cell differential expression
Squair, J. W., Gautier, M., Kathe, C., Anderson, M. A., James, N. D., Hutson, T. H., Hudelle, R., Qaiser, T., Matson, K. J. E., Barraud, Q., et al. (2021) · doi:10.1101/2021.03.12.435024 · Cited by 1,017 · see citing works
Cell type prioritization in single-cell data
Skinnider, M. A., Squair, J. W., Kathe, C., Anderson, M. A., Gautier, M., Matson, K. J. E., Milano, M., Hutson, T. H., Barraud, Q., Phillips, A. A., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0605-1 · Cited by 274 · see citing works
- Authors
- Aztekin, C., Hiscock, T. W., Marioni, J. C., Gurdon, J. B., Simons, B. D., & Jullien, J.
- Affiliations
- University of Cambridge (GB)
- European Bioinformatics Institute (GB)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- Corresponding author
- Aztekin, C.
- Hiscock, T. W.
- Simons, B. D.
- Jullien, J.
- Venue
- Science
- Published
- 2019-05-17
- Volume
- 364
- Issue
- 6441
- Pages
- 653-658
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6986927
- OpenAlex
- W2946771864
- Cited by
- 142
- References
- 44
- Citations by year
- 2026: 13 · 2025: 14 · 2024: 18 · 2023: 16 · 2022: 25 · 2021: 23 · 2020: 25 · 2019: 8
- FWCI
- 6.70
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Wellcome Trust
- Cancer Research UK
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Planarian Biology and Electrostimulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Health Sciences › Medicine › Rehabilitation › Wound Healing and Treatments
- Keywords
- tadpole tail regeneration, Xenopus, tail amputation, wound epidermis, single-cell RNA sequencing, cell fate specification, cell transplantation, tissue regeneration
- MeSH terms
- Epidermal Cells, Animals, Epidermis, Tail, Xenopus laevis, Sequence Analysis, RNA, Xenopus Proteins, Single-Cell Analysis, Transcriptome, Re-Epithelialization
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.
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
