| celltype | gene | reference |
|---|---|---|
| Proximal Mesenchyme (ProxMes) | Meis2, WT1 | Javier Capdevila, Tohru Tsukui, Concepción Rodríguez Esteban, Vincenzo Zappavigna, Juan Carlos Izpisúa Belmonte, Control of Vertebrate Limb Outgrowth by the Proximal Factor Meis2 and Distal Antagonism of BMPs by Gremlin, Molecular Cell,Volume 4, Issue 5,1999,Pages 839-849.; Moore, A. W. et al. YAC transgenic analysis reveals Wilms’ tumour 1 gene activity in the proliferating coelomic epithelium, developing diaphragm and limb. Mech. Dev. 79, (1998). |
| Mesenchyme 1 (Mes1) | Meis2 | Javier Capdevila, Tohru Tsukui, Concepción Rodríguez Esteban, Vincenzo Zappavigna, Juan Carlos Izpisúa Belmonte, Control of Vertebrate Limb Outgrowth by the Proximal Factor Meis2 and Distal Antagonism of BMPs by Gremlin, Molecular Cell,Volume 4, Issue 5,1999,Pages 839-849. |
| Mesenchyme 2 (Mes2) | KLF2 | Antin, P. B., Pier, M., Sesepasara, T., Yatskievych, T. A. & Darnell, D. K. Embryonic Expression of the Chicken Krüppel-like (KLF) Transcription Factor Gene Family. Dev. Dyn. 239, 1879 (2010) |
| Mesenchyme 3 (Mes3) | CITED1 | Dunwoodie SL, Rodriguez TA, Beddington RS. Msg1 and Mrg1, founding members of a gene family, show distinct patterns of gene expression during mouse embryogenesis. Mech Dev. 1998 Mar;72(1-2):27-40. |
| Mesenchyme 4 (Mes4) | PRAC1 | Hu, W. Y. et al. Isolation and functional interrogation of adult human prostate epithelial stem cells at single cell resolution. Stem Cell Res. 23, (2017). |
| ISL1+Mesenchyme (ISL1+Mes) | ISL1 | Yang L, Cai CL, Lin L, Qyang Y, Chung C, Monteiro RM, Mummery CL, Fishman GI, Cogen A, Evans S. Isl1Cre reveals a common Bmp pathway in heart and limb development. Development. 2006 Apr;133(8):1575-85. |
| Transitional Mesenchyme (TransMes) | IRX1, IRX2 | Díaz-Hernández ME, Bustamante M, Galván-Hernández CI, Chimal-Monroy J. Irx1 and Irx2 are coordinately expressed and regulated by retinoic acid, TGFβ and FGF signaling during chick hindlimb development. PLoS One. 2013;8(3):e58549. Zülch A, Becker MB, Gruss P. Expression pattern of Irx1 and Irx2 during mouse digit development. Mech Dev. 2001 Aug;106(1-2):159-62. |
| RDH10+ Distal Mesenchyme (RDH10+DistalMes) | RDH10 | Sandell LL, Sanderson BW, Moiseyev G, Johnson T, Mushegian A, Young K, Rey JP, Ma JX, Staehling-Hampton K, Trainor PA. RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development. Genes Dev. 2007 May 1;21(9):1113-24. |
| Distal Mesenchyme (DistalMes) | MSX1, LHX2 | Yang Y, Zhu X, Jia X, Hou W, Zhou G, Ma Z, Yu B, Pi Y, Zhang X, Wang J, Wang G. Phosphorylation of Msx1 promotes cell proliferation through the Fgf9/18-MAPK signaling pathway during embryonic limb development. Nucleic Acids Res. 2020 Nov 18;48(20):11452-11467. Hara K, Ide H. Msx1 expressing mesoderm is important for the apical ectodermal ridge (AER)-signal transfer in chick limb development. Dev Growth Differ. 1997 Dec;39(6):705-14. Rodriguez-Esteban C, Schwabe JW, Peña JD, Rincon-Limas DE, Magallón J, Botas J, Izpisúa Belmonte JC. Lhx2, a vertebrate homologue of apterous, regulates vertebrate limb outgrowth. Development. 1998 Oct;125(20):3925-34. |
| Mesencondensation cells (MesCond) | PAX9 | Mammoto T, Mammoto A, Torisawa YS, Tat T, Gibbs A, Derda R, Mannix R, de Bruijn M, Yung CW, Huh D, Ingber DE. Mechanochemical control of mesenchymal condensation and embryonic tooth organ formation. Dev Cell. 2011 Oct 18;21(4):758-69. |
| Osteochondral progenetor (OCP) | PRRX1 | He, J. et al. Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses. Cell Res. 31, 742–757 (2021). |
| InterZone | GDF5 | Roelofs AJ, Zupan J, Riemen AHK, Kania K, Ansboro S, White N, Clark SM, De Bari C. Joint morphogenetic cells in the adult mammalian synovium. Nat Commun. 2017 May 16;8:15040. |
| Chondrogenic Progenitor (ChondroProg) | SOX9, WWP2 | V. Lefebvre, M. Dvir-Ginzberg, SOX9 and the many facets of its regulation in the chondrocyte lineage. Connect. Tissue Res. 58 (2017), doi:10.1080/03008207.2016.1183667. Nakamura Y, Yamamoto K, He X, Otsuki B, Kim Y, Murao H, Soeda T, Tsumaki N, Deng JM, Zhang Z, Behringer RR, Crombrugghe Bd, Postlethwait JH, Warman ML, Nakamura T, Akiyama H. Wwp2 is essential for palatogenesis mediated by the interaction between Sox9 and mediator subunit 25. Nat Commun. 2011;2:251. |
| Resting Chondrocyte (RestingChon) | UCMA | A. Tagariello, J. Luther, M. Streiter, L. Didt-Koziel, M. Wuelling, C. Surmann-Schmitt, M. Stock, N. Adam, A. Vortkamp, A. Winterpacht, Ucma--A novel secreted factor represents a highly specific marker for distal chondrocytes. Matrix Biol. 27 (2008), doi:10.1016/j.matbio.2007.07.004 |
| Proliferating Chondrocyte (ProlifChon) | SOX9, COL2A1, G2/M/S cell cycle phase | Aghajanian, P. & Mohan, S. The art of building bone: emerging role of chondrocyte-to-osteoblast transdifferentiation in endochondral ossification. Bone Research 6, 1–9 (2018). |
| Prehypertrophic Chondrocyte (PrehyperChon) | IHH | B. St-Jacques, M. Hammerschmidt, A. P. McMahon, Indian hedgehog signaling regulates proliferation and differentiation of chondrocytes and is essential for bone formation. Genes Dev. 13 (1999), doi:10.1101/gad.13.16.2072 |
| Hypertrophic Chondrocyte (HyperChon) | COL10A1 | C. M. Kielty, A. P. Kwan, D. F. Holmes, S. L. Schor, M. E. Grant, Type X collagen, a product of hypertrophic chondrocytes. Biochem. J. 227 (1985), doi:10.1042/bj2270545 |
| Perichondrium (PeriChon) | THBS2 | R. P. Tucker, The in situ localization of tenascin splice variants and thrombospondin 2 mRNA in the avian embryo. Development. 117 (1993), doi:10.1242/dev.117.1.347 |
| Osteoblast (OsteoB) | RUNX2, SP7 | Liu DD, Zhang CY, Liu Y, Li J, Wang YX, Zheng SG. RUNX2 Regulates Osteoblast Differentiation via the BMP4 Signaling Pathway. J Dent Res. 2022 Sep;101(10):1227-1237.Hojo H, Ohba S. Sp7 Action in the Skeleton: Its Mode of Action, Functions, and Relevance to Skeletal Diseases. Int J Mol Sci. 2022 May 18;23(10):5647. |
| Articular Chondrocyte (ArtiChon) | PRG4 | Kozhemyakina E, Zhang M, Ionescu A, Ayturk UM, Ono N, Kobayashi A, Kronenberg H, Warman ML, Lassar AB. Identification of a Prg4-expressing articular cartilage progenitor cell population in mice. Arthritis Rheumatol. 2015 May;67(5):1261-73. Zhang CH, Gao Y, Jadhav U, Hung HH, Holton KM, Grodzinsky AJ, Shivdasani RA, Lassar AB. Creb5 establishes the competence for Prg4 expression in articular cartilage. Commun Biol. 2021 Mar 12;4(1):332. |
| Tendon Progenitor (TenoProg) | SCX | C. Shukunami, A. Takimoto, Y. Nishizaki, Y. Yoshimoto, S. Tanaka, S. Miura, H. Watanabe, T. Sakuma, T. Yamamoto, G. Kondoh, Y. Hiraki, Scleraxis is a transcriptional activator that regulates the expression of Tenomodulin, a marker of mature tenocytes and ligamentocytes. Sci. Rep. 8, 1–17 (2018). |
| Tenocyte (Teno) | TNMD | Xu P, Deng B, Zhang B, Luo Q, Song G. Stretch-Induced Tenomodulin Expression Promotes Tenocyte Migration via F-Actin and Chromatin Remodeling. Int J Mol Sci. 2021 May 6;22(9):4928. |
| Perimysium | GCG | *novel classification |
| PAX3+ Myogenic Progenitor (PAX3+MyoProg) | PAX3 | Buckingham M, Relaix F. PAX3 and PAX7 as upstream regulators of myogenesis. Semin Cell Dev Biol. 2015 Aug;44:115-25. |
| PAX7+ Myogenic Progenitor (PAX7+MyoProg) | PAX7 | Buckingham M, Relaix F. PAX3 and PAX7 as upstream regulators of myogenesis. Semin Cell Dev Biol. 2015 Aug;44:115-25. |
| Myoblast (MyoB1/MyoB2) | MYOD1 | iu Cj, Wang H, Zhao Z, Yu S, Lu YB, Meyer J, Chatterjee G, Deschamps S, Roe BA, Lengyel P. MyoD-dependent induction during myoblast differentiation of p204, a protein also inducible by interferon. Mol Cell Biol. 2000 Sep;20(18):7024-36. |
| Myocyte (MyoC1/MyoC2) | MYOG | Ganassi M, Badodi S, Ortuste Quiroga HP, Zammit PS, Hinits Y, Hughes SM. Myogenin promotes myocyte fusion to balance fibre number and size. Nat Commun. 2018 Oct 12;9(1):4232. |
| MYH3+ Myocyte (MYH3+MyoC) | MYH3 | Schiaffino S, Rossi AC, Smerdu V, Leinwand LA, Reggiani C. Developmental myosins: expression patterns and functional significance. Skelet Muscle. 2015 Jul 15;5:22. |
| MYL3+ Myocyte (MYL3+MyoC) | MYL3 | Schiaffino S, Rossi AC, Smerdu V, Leinwand LA, Reggiani C. Developmental myosins: expression patterns and functional significance. Skelet Muscle. 2015 Jul 15;5:22. |
| Intermediate Muscular Fibroblast （InterMusFibro） | ALDH1A3, MYH3 | *novel classification |
| ADH+ Fibroblast (ADH+Fibro) | ADH1B, ALDH1A3 | *novel classification |
| STMN2+ Fibroblast (STMN2+Fibro) | STMN2 | *novel classification |
| MFAP5+ Fibroblast (MFAP5+Fibro) | MFAP5 | Barbier M, Gross MS, Aubart M, Hanna N, Kessler K, Guo DC, Tosolini L, Ho-Tin-Noe B, Regalado E, Varret M, Abifadel M, Milleron O, Odent S, Dupuis-Girod S, Faivre L, Edouard T, Dulac Y, Busa T, Gouya L, Milewicz DM, Jondeau G, Boileau C. MFAP5 loss-of-function mutations underscore the involvement of matrix alteration in the pathogenesis of familial thoracic aortic aneurysms and dissections. Am J Hum Genet. 2014 Dec 4;95(6):736-43. |
| HOXC5+ Dermal Fibroblast Progenitor (HOXC5+DermFibroProg) | HOXC5 | *novel classification |
| F10+ Dermal Fibroblast Progenitor (F10+DermFibroProg) | F10 | *novel classification |
| Dermal Fibroblast (DermFibro) | TWIST2 | V. Thulabandu, D. Chen, R. P. Atit, Dermal fibroblast in cutaneous development and healing. Wiley Interdiscip. Rev. Dev. Biol. 7 (2018), doi:10.1002/wdev.307 |
| Smooth Muscle Progenitor (SMProg) | IGFBP7 | Karlsson, M. et al. A single-cell type transcriptomics map of human tissues. Science advances 7, (2021). |
| Smooth Muscle (SMC) | PLN, ACTA2 | Perisic Matic L, Rykaczewska U, Razuvaev A, Sabater-Lleal M, Lengquist M, Miller CL, Ericsson I, Röhl S, Kronqvist M, Aldi S, Magné J, Paloschi V, Vesterlund M, Li Y, Jin H, Diez MG, Roy J, Baldassarre D, Veglia F, Humphries SE, de Faire U, Tremoli E, Odeberg J, Vukojević V, Lehtiö J, Maegdefessel L, Ehrenborg E, Paulsson-Berne G, Hansson GK, Lindeman JH, Eriksson P, Quertermous T, Hamsten A, Hedin U. Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM. Arterioscler Thromb Vasc Biol. 2016 Sep;36(9):1947-61. J. Vandekerckhove, K. Weber, At least six different actins are expressed in a higher mammal: an analysis based on the amino acid sequence of the amino-terminal tryptic peptide. J. Mol. Biol. 126 (1978), doi:10.1016/0022-2836(78)90020-7 |
| Pericyte | KCNJ8 | Bondjers C, He L, Takemoto M, Norlin J, Asker N, Hellström M, Lindahl P, Betsholtz C. Microarray analysis of blood microvessels from PDGF-B and PDGF-Rbeta mutant mice identifies novel markers for brain pericytes. FASEB J. 2006 Aug;20(10):1703-5. |
| Neural Fibroblast (NeuralFibro) | FOXS1, PI16 | Singhmar P, Trinh RTP, Ma J, Huo X, Peng B, Heijnen CJ, Kavelaars A. The fibroblast-derived protein PI16 controls neuropathic pain. Proc Natl Acad Sci U S A. 2020 Mar 10;117(10):5463-5471. |
| Neuronal | SST | Urban-Ciecko J, Barth AL. Somatostatin-expressing neurons in cortical networks. Nat Rev Neurosci. 2016 Jul;17(7):401-9. |
| Schwann Progenitor (SchwannProg) | MPZ | Z. Liu, Y.-Q. Jin, L. Chen, Y. Wang, X. Yang, J. Cheng, W. Wu, Z. Qi, Z. Shen, Specific Marker Expression and Cell State of Schwann Cells during Culture In Vitro. PLoS One. 10 (2015), doi:10.1371/journal.pone.0123278. |
| Schwann | MPZ, MBP | Z. Liu, Y.-Q. Jin, L. Chen, Y. Wang, X. Yang, J. Cheng, W. Wu, Z. Qi, Z. Shen, Specific Marker Expression and Cell State of Schwann Cells during Culture In Vitro. PLoS One. 10 (2015), doi:10.1371/journal.pone.0123278. |
| Synaptic Schwann (SynapSchwann) | COL20A1 | Castro R, Taetzsch T, Vaughan SK, Godbe K, Chappell J, Settlage RE, Valdez G. Specific labeling of synaptic schwann cells reveals unique cellular and molecular features. Elife. 2020 Jun 25;9:e56935. |
| Melanocyte (Melano) | MLANA | Du J, Miller AJ, Widlund HR, Horstmann MA, Ramaswamy S, Fisher DE. MLANA/MART1 and SILV/PMEL17/GP100 are transcriptionally regulated by MITF in melanocytes and melanoma. Am J Pathol. 2003 Jul;163(1):333-43. |
| Periderm | KRT4 | Teixeira Rosa J, Oralová V, Larionova D, Eisenhoffer GT, Eckhard Witten P, Huysseune A. Periderm invasion contributes to epithelial formation in the teleost pharynx. Sci Rep. 2019 Jul 12;9(1):10082. |
| Basal | GJB6 | Liu W, Rask-Andersen H. GJB2 and GJB6 gene transcripts in the human cochlea: A study using RNAscope, confocal, and super-resolution structured illumination microscopy. Front Mol Neurosci. 2022 Sep 20;15:973646. |
| Apical Ectodermal Ridge Basal (AER-Basal) | FGF8 | Lewandoski M, Sun X, Martin GR. Fgf8 signalling from the AER is essential for normal limb development. Nat Genet. 2000 Dec;26(4):460-3. |
| Arterial Endothelial (ArterialEndo) | PRND | Chen Z, Morales JE, Avci N, Guerrero PA, Rao G, Seo JH, McCarty JH. The vascular endothelial cell-expressed prion protein doppel promotes angiogenesis and blood-brain barrier development. Development. 2020 Sep 23;147(18):dev193094. |
| Venous Endothelial (VenousEndo) | PLVAP | Herrnberger L, Ebner K, Junglas B, Tamm ER. The role of plasmalemma vesicle-associated protein (PLVAP) in endothelial cells of Schlemm's canal and ocular capillaries. Exp Eye Res. 2012 Dec;105:27-33. |
| Lymphoendothelial (LymphEndo) | CCL21 | Johnson LA, Jackson DG. Inflammation-induced secretion of CCL21 in lymphatic endothelium is a key regulator of integrin-mediated dendritic cell transmigration. Int Immunol. 2010 Oct;22(10):839-49. |
| Lymphoid-primed multipotent progenitor (LMPP)/Early lymphoid progenitors(ELP) | IL7R | Iwasaki H, Akashi K. Myeloid lineage commitment from the hematopoietic stem cell. Immunity. 2007 Jun;26(6):726-40. |
| common myeloid progenitors/Granulocyte-monocyte progenitors (GMPs) | PRTN3 | Karatepe K, Zhu H, Zhang X, Guo R, Kambara H, Loison F, Liu P, Yu H, Ren Q, Luo X, Manis J, Cheng T, Ma F, Xu Y, Luo HR. Proteinase 3 Limits the Number of Hematopoietic Stem and Progenitor Cells in Murine Bone Marrow. Stem Cell Reports. 2018 Nov 13;11(5):1092-1105. |
| Natural killer (NK) | KLRC1 | Bongen E, Vallania F, Utz PJ, Khatri P. KLRD1-expressing natural killer cells predict influenza susceptibility. Genome Med. 2018 Jun 14;10(1):45. |
| B | CD79B | Takeuchi T, Yamaguchi M, Kobayashi K, Miyazaki K, Tawara I, Imai H, Ono R, Nosaka T, Tanaka K, Katayama N. MYD88, CD79B, and CARD11 gene mutations in CD5-positive diffuse large B-cell lymphoma. Cancer. 2017 Apr 1;123(7):1166-1173. |
| Myelocyte | CAMP | Gombart AF, Borregaard N, Koeffler HP. Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3. FASEB J. 2005 Jul;19(9):1067-77. |
| Dendritic Cell 2 (DC2) | CLEC10A | Heger L, Balk S, Lühr JJ, Heidkamp GF, Lehmann CHK, Hatscher L, Purbojo A, Hartmann A, Garcia-Martin F, Nishimura SI, Cesnjevar R, Nimmerjahn F, Dudziak D. CLEC10A Is a Specific Marker for Human CD1c+ Dendritic Cells and Enhances Their Toll-Like Receptor 7/8-Induced Cytokine Secretion. Front Immunol. 2018 Apr 27;9:744. |
| Monocyte | S100A12 | Foell D, Wittkowski H, Kessel C, Lüken A, Weinhage T, Varga G, Vogl T, Wirth T, Viemann D, Björk P, van Zoelen MA, Gohar F, Srikrishna G, Kraft M, Roth J. Proinflammatory S100A12 can activate human monocytes via Toll-like receptor 4. Am J Respir Crit Care Med. 2013 Jun 15;187(12):1324-34. |
| Macrophage (Macro) | C1QA | Tran MTN, Hamada M, Jeon H, Shiraishi R, Asano K, Hattori M, Nakamura M, Imamura Y, Tsunakawa Y, Fujii R, Usui T, Kulathunga K, Andrea CS, Koshida R, Kamei R, Matsunaga Y, Kobayashi M, Oishi H, Kudo T, Takahashi S. MafB is a critical regulator of complement component C1q. Nat Commun. 2017 Nov 22;8(1):1700. |
| Mast | TPSB2 | Kalesnikoff J, Galli SJ. New developments in mast cell biology. Nat Immunol. 2008 Nov;9(11):1215-23. |
| Megakaryocyte (Megakaryo) | CLEC1B | Otake S, Sasaki T, Shirai T, Tsukiji N, Tamura S, Takano K, Ozaki Y, Suzuki-Inoue K. CLEC-2 stimulates IGF-1 secretion from podoplanin-positive stromal cells and positively regulates erythropoiesis in mice. J Thromb Haemost. 2021 Jun;19(6):1572-1584. |
| Definite Erythrocyte (DefErythro) | HBB | Jain, V. et al. Single Cell RNA-Seq Analysis of Human Red Cells. Front. Physiol. 13, (2022). |
| Definite Reticulocyte (DefReticulo) | TSPO2 | Marginedas-Freixa I, Hattab C, Bouyer G, Halle F, Chene A, Lefevre SD, Cambot M, Cueff A, Schmitt M, Gamain B, Lacapere JJ, Egee S, Bihel F, Le Van Kim C, Ostuni MA. TSPO ligands stimulate ZnPPIX transport and ROS accumulation leading to the inhibition of P. falciparum growth in human blood. Sci Rep. 2016 Sep 19;6:33516. |
| Primitive Erythrocyte 1 (PrimErythro1) | UCA1 | Liu J, Li Y, Tong J, Gao J, Guo Q, Zhang L, Wang B, Zhao H, Wang H, Jiang E, Kurita R, Nakamura Y, Tanabe O, Engel JD, Bresnick EH, Zhou J, Shi L. Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. Nat Commun. 2018 Oct 22;9(1):4386. |
| Primitive Erythrocyte 2 (PrimErythro2) | HBE1 | Weiss MJ, Zhou S, Feng L, Gell DA, Mackay JP, Shi Y, Gow AJ. Role of alpha-hemoglobin-stabilizing protein in normal erythropoiesis and beta-thalassemia. Ann N Y Acad Sci. 2005;1054:103-17. |