Single-cell RNA-seq and ATAC-seq Regeneration Portal

This database is a collection of single cell RNA-seq and ATAC-seq data for regeneration experiments.




DATASETS
101
REFERENCES
69
VISITORS
524

Full reference list:

  1. A. A. Cutler, B. Pawlikowski, J. R. Wheeler, et al. “The regenerating skeletal muscle niche drives satellite cell return to quiescence”. Eng. In: iScience 25.6 (Jun. 2022), p. 104444. ISSN: 2589-0042. DOI: 10.1016/j.isci.2022.104444. PMID: 35733848.

  2. A. Ayyaz, S. Kumar, B. Sangiorgi, et al. “Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell”. Eng. In: Nature 569.7754 (May. 2019), pp. 121-125. ISSN: 1476-4687. DOI: 10.1038/s41586-019-1154-y. PMID: 31019301.

  3. A. D. Kakebeen, A. D. Chitsazan, M. C. Williams, et al. “Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors”. Eng. In: eLife 9 (Apr. 2020). ISSN: 2050-084X. DOI: 10.7554/eLife.52648. PMID: 32338593.

  4. A. Jacobi, N. M. Tran, W. Yan, et al. “Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells”. Eng. In: Neuron 110.16 (Aug. 2022), pp. 2625-2645.e7. ISSN: 1097-4199. DOI: 10.1016/j.neuron.2022.06.002. PMID: 35767994.

  5. A. O. Granillo, D. Zamora, R. R. Schnittker, et al. “Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration”. Eng. In: iScience 27.9 (Sep. 2024), p. 110737. ISSN: 2589-0042. DOI: 10.1016/j.isci.2024.110737. PMID: 39286507.

  6. A. Ortega Granillo, D. Zamora, R. R. Schnittker, et al. “Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration”. In: iScience 27.9 (Sep. 2024), p. 110737. ISSN: 2589-0042. DOI: 10.1016/j.isci.2024.110737. URL: http://dx.doi.org/10.1016/j.isci.2024.110737.

  7. A. Ruiz-Villalba, J. P. Romero, S. C. Hernández, et al. “Single-Cell RNA Sequencing Analysis Reveals a Crucial Role for CTHRC1 (Collagen Triple Helix Repeat Containing 1) Cardiac Fibroblasts After Myocardial Infarction”. Eng. In: Circulation 142.19 (Nov. 2020), pp. 1831-1847. ISSN: 1524-4539. DOI: 10.1161/CIRCULATIONAHA.119.044557. PMID: 32972203.

  8. A. W. Stockinger, L. Adelmann, M. Fahrenberger, et al. “Molecular profiles, sources and lineage restrictions of stem cells in an annelid regeneration model”. In: Nature Communications 15.1 (Nov. 2024). ISSN: 2041-1723. DOI: 10.1038/s41467-024-54041-3. URL: http://dx.doi.org/10.1038/s41467-024-54041-3.

  9. C. Aztekin, T. W. Hiscock, J. C. Marioni, et al. “Identification of a regeneration-organizing cell in the Xenopus tail”. Eng. In: Science (New York, N.Y.) 364.6441 (May. 2019), pp. 653-658. ISSN: 1095-9203. DOI: 10.1126/science.aav9996. PMID: 31097661.

  10. C. Li, Z. Wu, L. Zhou, et al. “Temporal and spatial cellular and molecular pathological alterations with single-cell resolution in the adult spinal cord after injury”. Eng. In: Signal transduction and targeted therapy 7.1 (Mar. 2022), p. 65. ISSN: 2059-3635. DOI: 10.1038/s41392-022-00885-4. PMID: 35232960.

  11. C. M. Carey, H. L. Hollins, A. V. Schmid, et al. “Distinct features of the regenerating heart uncovered through comparative single-cell profiling”. Eng. In: Biology open 13.4 (Apr. 2024). ISSN: 2046-6390. DOI: 10.1242/bio.060156. PMID: 38526188.

  12. C. Morral, A. Ayyaz, H. Kuo, et al. “p53 promotes revival stem cells in the regenerating intestine after severe radiation injury”. In: Nature Communications 15.1 (Apr. 2024). ISSN: 2041-1723. DOI: 10.1038/s41467-024-47124-8. URL: http://dx.doi.org/10.1038/s41467-024-47124-8.

  13. D. A. Skelly, G. T. Squiers, M. A. McLellan, et al. “Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart”. Eng. In: Cell reports 22.3 (Jan. 2018), pp. 600-610. ISSN: 2211-1247. DOI: 10.1016/j.celrep.2017.12.072. PMID: 29346760.

  14. D. Bormann, M. Knoflach, E. Poreba, et al. “Single-nucleus RNA sequencing reveals glial cell type-specific responses to ischemic stroke in male rodents”. In: Nature Communications 15.1 (Jul. 2024). ISSN: 2041-1723. DOI: 10.1038/s41467-024-50465-z. URL: http://dx.doi.org/10.1038/s41467-024-50465-z.

  15. D. K. Shaw, V. M. Saraswathy, L. Zhou, et al. “Localized EMT reprograms glial progenitors to promote spinal cord repair”. Eng. In: Developmental cell 56.5 (Mar. 2021), pp. 613-626.e7. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2021.01.017. PMID: 33609461.

  16. D. W. McKellar, L. D. Walter, L. T. Song, et al. “Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration”. Eng. In: Communications biology 4.1 (Nov. 2021), p. 1280. ISSN: 2399-3642. DOI: 10.1038/s42003-021-02810-x. PMID: 34773081.

  17. E. Llorens-Bobadilla, J. M. Chell, P. Le Merre, et al. “A latent lineage potential in resident neural stem cells enables spinal cord repair”. Eng. In: Science (New York, N.Y.) 370.6512 (Oct. 2020). ISSN: 1095-9203. DOI: 10.1126/science.abb8795. PMID: 33004487.

  18. F. H. Brennan, Y. Li, C. Wang, et al. “Microglia coordinate cellular interactions during spinal cord repair in mice”. Eng. In: Nature communications 13.1 (Jul. 2022), p. 4096. ISSN: 2041-1723. DOI: 10.1038/s41467-022-31797-0. PMID: 35835751.

  19. F. Sun, J. Ou, A. R. Shoffner, et al. “Enhancer selection dictates gene expression responses in remote organs during tissue regeneration”. In: Nature Cell Biology 24.5 (May. 2022), p. 685–696. ISSN: 1476-4679. DOI: 10.1038/s41556-022-00906-y. URL: http://dx.doi.org/10.1038/s41556-022-00906-y.

  20. G. L. Johnson, E. J. Masias, and J. A. Lehoczky. “Cellular Heterogeneity and Lineage Restriction during Mouse Digit Tip Regeneration at Single-Cell Resolution”. Eng. In: Developmental cell 52.4 (Feb. 2020), pp. 525-540.e5. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2020.01.026. PMID: 32097654.

  21. H. Honkoop, D. E. de Bakker, A. Aharonov, et al. “Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart”. Eng. In: eLife 8 (Dec. 2019). ISSN: 2050-084X. DOI: 10.7554/eLife.50163. PMID: 31868166.

  22. J. Sun, E. A. Peterson, A. Z. Wang, et al. “hapln1 Defines an Epicardial Cell Subpopulation Required for Cardiomyocyte Expansion During Heart Morphogenesis and Regeneration”. Eng. In: Circulation 146.1 (Jul. 2022), pp. 48-63. ISSN: 1524-4539. DOI: 10.1161/CIRCULATIONAHA.121.055468. PMID: 35652354.

  23. J. V. Kurland, A. A. Cutler, J. T. Stanley, et al. “Aging disrupts gene expression timing during muscle regeneration”. Eng. In: Stem cell reports 18.6 (Jun. 2023), pp. 1325-1339. ISSN: 2213-6711. DOI: 10.1016/j.stemcr.2023.05.005. PMID: 37315524.

  24. J. Wen, G. P. Mercado, A. Volland, et al. “Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine”. Eng. In: Science advances 7.30 (Jul. 2021). ISSN: 2375-2548. DOI: 10.1126/sciadv.abg1371. PMID: 34301599.

  25. K. Lust, A. Maynard, T. Gomes, et al. “Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration”. Eng. In: Science (New York, N.Y.) 377.6610 (Sep. 2022), p. eabp9262. ISSN: 1095-9203. DOI: 10.1126/science.abp9262. PMID: 36048956.

  26. L. Cavone, T. McCann, L. K. Drake, et al. “A unique macrophage subpopulation signals directly to progenitor cells to promote regenerative neurogenesis in the zebrafish spinal cord”. Eng. In: Developmental cell 56.11 (Jun. 2021), pp. 1617-1630.e6. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2021.04.031. PMID: 34033756.

  27. L. Chen, X. Qiu, A. Dupre, et al. “TGFB1 induces fetal reprogramming and enhances intestinal regeneration”. Eng. In: Cell stem cell 30.11 (Nov. 2023), pp. 1520-1537.e8. ISSN: 1875-9777. DOI: 10.1016/j.stem.2023.09.015. PMID: 37865088.

  28. L. Li, L. Cui, P. Lin, et al. “Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers”. Eng. In: Cell stem cell 30.3 (Mar. 2023), pp. 283-299.e9. ISSN: 1875-9777. DOI: 10.1016/j.stem.2023.01.009. PMID: 36787740.

  29. L. M. Milich, J. S. Choi, C. Ryan, et al. “Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord”. Eng. In: The Journal of experimental medicine 218.8 (Aug. 2021). ISSN: 1540-9538. DOI: 10.1084/jem.20210040. PMID: 34132743.

  30. L. Wang, P. Yu, B. Zhou, et al. “Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function”. Eng. In: Nature cell biology 22.1 (Jan. 2020), pp. 108-119. ISSN: 1476-4679. DOI: 10.1038/s41556-019-0446-7. PMID: 31915373.

  31. Lu H, Yan H, Xing Y, et al. Single-Cell Map of Dynamic Multicellular Ecosystem of Radiation-Induced Intestinal Injury. bioRxiv; 2023. DOI: 10.1101/2023.03.06.531402

  32. M. A. Storer, N. Mahmud, K. Karamboulas, et al. “Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration”. Eng. In: Developmental cell 52.4 (Feb. 2020), pp. 509-524.e9. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2019.12.004. PMID: 31902657.

  33. M. Cui, Z. Wang, K. Chen, et al. “Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing”. Eng. In: Developmental cell 53.1 (Apr. 2020), pp. 102-116.e8. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2020.02.019. PMID: 32220304.

  34. M. Fink, K. Njah, S. J. Patel, et al. “Chromatin remodelling in damaged intestinal crypts orchestrates redundant TGFβ and Hippo signalling to drive regeneration”. In: Nature Cell Biology (Nov. 2024). ISSN: 1476-4679. DOI: 10.1038/s41556-024-01550-4. URL: http://dx.doi.org/10.1038/s41556-024-01550-4.

  35. M. J. Carr, J. S. Toma, A. P. W. Johnston, et al. “Mesenchymal Precursor Cells in Adult Nerves Contribute to Mammalian Tissue Repair and Regeneration”. Eng. In: Cell stem cell 24.2 (Feb. 2019), pp. 240-256.e9. ISSN: 1875-9777. DOI: 10.1016/j.stem.2018.10.024. PMID: 30503141.

  36. M. Litviňuková, C. Talavera-López, H. Maatz, et al. “Cells of the adult human heart”. Eng. In: Nature 588.7838 (Dec. 2020), pp. 466-472. ISSN: 1476-4687. DOI: 10.1038/s41586-020-2797-4. PMID: 32971526.

  37. M. Zamboni, E. Llorens-Bobadilla, J. P. Magnusson, et al. “A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury”. Eng. In: Cell stem cell 27.4 (Oct. 2020), pp. 605-617.e5. ISSN: 1875-9777. DOI: 10.1016/j.stem.2020.07.006. PMID: 32758425.

  38. N. R. Tucker, M. Chaffin, S. J. Fleming, et al. “Transcriptional and Cellular Diversity of the Human Heart”. Eng. In: Circulation 142.5 (Aug. 2020), pp. 466-482. ISSN: 1524-4539. DOI: 10.1161/CIRCULATIONAHA.119.045401. PMID: 32403949.

  39. O. Avraham, P. Deng, S. Jones, et al. “Satellite glial cells promote regenerative growth in sensory neurons”. Eng. In: Nature communications 11.1 (Sep. 2020), p. 4891. ISSN: 2041-1723. DOI: 10.1038/s41467-020-18642-y. PMID: 32994417.

  40. O. Avraham, R. Feng, E. E. Ewan, et al. “Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair”. Eng. In: eLife 10 (Sep. 2021). ISSN: 2050-084X. DOI: 10.7554/eLife.68457. PMID: 34586065.

  41. Q. Yu, H. E. Walters, G. Pasquini, et al. “Cellular senescence promotes progenitor cell expansion during axolotl limb regeneration”. In: Developmental Cell 58.22 (Nov. 2023), pp. 2416-2427.e7. ISSN: 1534-5807. DOI: 10.1016/j.devcel.2023.09.009. URL: http://dx.doi.org/10.1016/j.devcel.2023.09.009.

  42. R. Satija, J. A. Farrell, D. Gennert, et al. “Spatial reconstruction of single-cell gene expression data”. Eng. In: Nature biotechnology 33.5 (May. 2015), pp. 495-502. ISSN: 1546-1696. DOI: 10.1038/nbt.3192. PMID: 25867923.

  43. S. N. Oprescu, F. Yue, J. Qiu, et al. “Temporal Dynamics and Heterogeneity of Cell Populations during Skeletal Muscle Regeneration”. Eng. In: iScience 23.4 (Apr. 2020), p. 100993. ISSN: 2589-0042. DOI: 10.1016/j.isci.2020.100993. PMID: 32248062.

  44. S. Sinha, H. D. Sparks, E. Labit, et al. “Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer”. Eng. In: Cell 185.25 (Dec. 2022), pp. 4717-4736.e25. ISSN: 1097-4172. DOI: 10.1016/j.cell.2022.11.004. PMID: 36493752.

  45. T. Gerber, P. Murawala, D. Knapp, et al. “Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration”. Eng. In: Science (New York, N.Y.) 362.6413 (Oct. 2018). ISSN: 1095-9203. DOI: 10.1126/science.aaq0681. PMID: 30262634.

  46. T. Hoang, J. Wang, P. Boyd, et al. “Gene regulatory networks controlling vertebrate retinal regeneration”. Eng. In: Science (New York, N.Y.) 370.6519 (Nov. 2020). ISSN: 1095-9203. DOI: 10.1126/science.abb8598. PMID: 33004674.

  47. U. V. Chembazhi, S. Bangru, M. Hernaez, et al. “Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver”. Eng. In: Genome research 31.4 (Apr. 2021), pp. 576-591. ISSN: 1549-5469. DOI: 10.1101/gr.267013.120. PMID: 33649154.

  48. V. Cigliola, A. Shoffner, N. Lee, et al. “Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer”. Eng. In: Nature communications 14.1 (Aug. 2023), p. 4857. ISSN: 2041-1723. DOI: 10.1038/s41467-023-40486-5. PMID: 37567873.

  49. V. M. Lewis, H. K. Le Bleu, A. L. Henner, et al. “Insulin-like growth factor receptor / mTOR signaling elevates global translation to accelerate zebrafish fin regenerative outgrowth”. In: Developmental Biology 502 (Oct. 2023), p. 1–13. ISSN: 0012-1606. DOI: 10.1016/j.ydbio.2023.05.008. URL: http://dx.doi.org/10.1016/j.ydbio.2023.05.008.

  50. V. M. Saraswathy, L. Zhou, and M. H. Mokalled. “Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair”. In: Nature Communications 15.1 (Aug. 2024). ISSN: 2041-1723. DOI: 10.1038/s41467-024-50628-y. URL: http://dx.doi.org/10.1038/s41467-024-50628-y.

  51. V. Moiseeva, A. Cisneros, V. Sica, et al. “Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration”. Eng. In: Nature 613.7942 (Jan. 2023), pp. 169-178. ISSN: 1476-4687. DOI: 10.1038/s41586-022-05535-x. PMID: 36544018.

  52. W. J. Tang, C. J. Watson, T. Olmstead, et al. “Single-cell resolution of MET- and EMT-like programs in osteoblasts during zebrafish fin regeneration”. Eng. In: iScience 25.2 (Feb. 2022), p. 103784. ISSN: 2589-0042. DOI: 10.1016/j.isci.2022.103784. PMID: 35169687.

  53. W. R. Karthaus, M. Hofree, D. Choi, et al. “Regenerative potential of prostate luminal cells revealed by single-cell analysis”. Eng. In: Science (New York, N.Y.) 368.6490 (May. 2020), pp. 497-505. ISSN: 1095-9203. DOI: 10.1126/science.aay0267. PMID: 32355025.

  54. W. Wang, C. Hu, A. Zeng, et al. “Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates”. Eng. In: Science (New York, N.Y.) 369.6508 (Sep. 2020). ISSN: 1095-9203. DOI: 10.1126/science.aaz3090. PMID: 32883834.

  55. W. Wang, C. Hu, A. Zeng, et al. “Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates”. In: Science 369.6508 (Sep. 2020). ISSN: 1095-9203. DOI: 10.1126/science.aaz3090. URL: http://dx.doi.org/10.1126/science.aaz3090.

  56. X. He, Z. Wang, L. Cheng, et al. “An antagonistic role of clock genes and lima1 in kidney regeneration”. In: Communications Biology 8.1 (Jan. 2025). ISSN: 2399-3642. DOI: 10.1038/s42003-025-07455-8. URL: http://dx.doi.org/10.1038/s42003-025-07455-8.

  57. X. Sheng, Z. Lin, C. Lv, et al. “Cycling Stem Cells Are Radioresistant and Regenerate the Intestine”. Eng. In: Cell reports 32.4 (Jul. 2020), p. 107952. ISSN: 2211-1247. DOI: 10.1016/j.celrep.2020.107952. PMID: 32726617.

  58. X. Xue, X. Wu, Y. Fan, et al. “Heterogeneous fibroblasts contribute to fibrotic scar formation after spinal cord injury in mice and monkeys”. In: Nature Communications 15.1 (Jul. 2024). ISSN: 2041-1723. DOI: 10.1038/s41467-024-50564-x. URL: http://dx.doi.org/10.1038/s41467-024-50564-x.

  59. Y. Atsuta, C. Lee, A. R. Rodrigues, et al. “Direct reprogramming of non-limb fibroblasts to cells with properties of limb progenitors”. Eng. In: Developmental cell 59.3 (Feb. 2024), pp. 415-430.e8. ISSN: 1878-1551. DOI: 10.1016/j.devcel.2023.12.010. PMID: 38320485.

  60. Y. Chen, Y. Hou, Q. Zeng, et al. “Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution”. Eng. In: Genome research 35.1 (Jan. 2025), pp. 202-218. ISSN: 1549-5469. DOI: 10.1101/gr.279372.124. PMID: 39809530.

  61. Y. Dong, Y. Yang, H. Wang, et al. “Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells”. Eng. In: Science advances 10.8 (Feb. 2024), p. eadk4694. ISSN: 2375-2548. DOI: 10.1126/sciadv.adk4694. PMID: 38381829.

  62. Y. Hou, H. J. Lee, Y. Chen, et al. “Cellular diversity of the regenerating caudal fin”. Eng. In: Science advances 6.33 (Aug. 2020), p. eaba2084. ISSN: 2375-2548. DOI: 10.1126/sciadv.aba2084. PMID: 32851162.

  63. Y. Hou, H. J. Lee, Y. Chen, et al. “Cellular diversity of the regenerating caudal fin”. In: Science Advances 6.33 (Aug. 2020). ISSN: 2375-2548. DOI: 10.1126/sciadv.aba2084. URL: http://dx.doi.org/10.1126/sciadv.aba2084.

  64. Y. Li, X. He, R. Kawaguchi, et al. “Microglia-organized scar-free spinal cord repair in neonatal mice”. Eng. In: Nature 587.7835 (Nov. 2020), pp. 613-618. ISSN: 1476-4687. DOI: 10.1038/s41586-020-2795-6. PMID: 33029008.

  65. Y. Nakada, Y. Zhou, W. Gong, et al. “Single Nucleus Transcriptomics: Apical Resection in Newborn Pigs Extends the Time Window of Cardiomyocyte Proliferation and Myocardial Regeneration”. Eng. In: Circulation 145.23 (Jun. 2022), pp. 1744-1747. ISSN: 1524-4539. DOI: 10.1161/CIRCULATIONAHA.121.056995. PMID: 35666813.

  66. Y. Xia, S. Duca, B. Perder, et al. “Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration”. Eng. In: Nature communications 13.1 (Dec. 2022), p. 7704. ISSN: 2041-1723. DOI: 10.1038/s41467-022-35433-9. PMID: 36513650.

  67. Z. Chi, S. Chen, D. Yang, et al. “Gasdermin D-mediated metabolic crosstalk promotes tissue repair”. In: Nature 634.8036 (Sep. 2024), p. 1168–1177. ISSN: 1476-4687. DOI: 10.1038/s41586-024-08022-7. URL: http://dx.doi.org/10.1038/s41586-024-08022-7.

  68. Z. Wang, M. Cui, A. M. Shah, et al. “Cell-Type-Specific Gene Regulatory Networks Underlying Murine Neonatal Heart Regeneration at Single-Cell Resolution”. Eng. In: Cell reports 33.10 (Dec. 2020), p. 108472. ISSN: 2211-1247. DOI: 10.1016/j.celrep.2020.108472. PMID: 33296652.

  69. Cortada, E., Yao, J., Xia, Y., Dundar, F., Zumbo, P., Yang, B., ... & Lo, J. (2023). Cross-species single-cell comparison of systemic and cardiac inflammatory responses after cardiac injury. bioRxiv, 2023-03.

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scRNAseq/scATACseq database (Version: 1.7.13 ) © 2024 - 2025 posslab@morgridge