Maker genes in some papers(update)

Tissue CellType Gene Full Name Gene Symbol Reference
Epididymal Epithelial cells Principal cell Aquaporin9 Aqp9 [1-3]
Epididymal Epithelial cells Principal cell CF Transmembrane Conductance Regulator Cftr [4, 5]
Epididymal Epithelial cells Basal cell Keratin 5 Krt5 [1, 2, 6, 7]
Epididymal Epithelial cells Basal cell Claudin-1 Cldn1 [7, 8]
Epididymal Epithelial cells Clear cell V-ATPa s e B1 subuni t Atp6v1b1 [2-4, 7]
Epididymal Epithelial cells Clear cell Forkhead Box I1 Foxi1 [9]
Epididymal Epithelial cells Narrow cell Carbonic anhydrase II Car2 [9]
Epididymal Epithelial cells Narrow cell Forkhead Box I1 Foxi1 [9]
Epididymal Epithelial cells Narrow cell CD4 antigen Cd4 [10]
Epididymal Epithelial cells Narrow cell CD8 antigen, alpha chain Cd8a [10]
Non-epithelial cells Spermatozoa Transition Protein 2 Tnp2 [11]
Non-epithelial cells Spermatozoa Transition Protein 1 Tnp1 [11, 12]
Non-epithelial cells Myoid cell Actin Alpha 2, Smooth Muscle Acta2 [13-15]
Non-epithelial cells Myoid cell Myosin Heavy Chain 11 Myh11 [16]
Non-epithelial cells Fibroblasts Collagen Type I Alpha 1 Chain Col1a1 [13]
Non-epithelial cells Macrophages Adhesion G Protein-Coupled Receptor E1 F4/80,Adgre1 [1, 6, 17-19]
Non-epithelial cells Macrophages Integrin subunit alpha M Itgam [18-20]
Non-epithelial cells Macrophages CD68 Molecule Cd68 [17, 19, 20]
Non-epithelial cells Monocytes Colony stimulating factor 1 receptor Cd115,Csf1r [13]
Non-epithelial cells Monocytes Lysozyme 2 Lyz2 [13]
Non-epithelial cells Endothelial Platelet And Endothelial Cell Adhesion Molecule 1 Pecam1 [21, 22]
Non-epithelial cells Endothelial Endoglin Eng [21, 22]
Non-epithelial cells Endothelial Cadherin 5 Cdh5 [13, 21, 22]
Non-epithelial cells Erythrocyte(Red blood cells) Hemoglobin Subunit Alpha 1 Hba-a1 [21]
Non-epithelial cells Erythrocyte(Red blood cells) Hemoglobin Subunit Alpha 2 Hba-a2 [21]
Non-epithelial cells Erythrocyte(Red blood cells) hemoglobin, beta adult s chain Hbb-bs [21]
1.  Zhu, W.,  et  al.,  Pattern  recognition  receptor-initiated  innate  antiviral  responses  in  mouse 
epididymal epithelial cells. J Immunol, 2015. 194(10): p. 4825-35. 
2.  Carvajal, G., et al., Impaired male fertility and abnormal epididymal epithelium differentiation 
in mice lacking CRISP1 and CRISP4. Sci Rep, 2018. 8(1): p. 17531. 
3.  Krapf, D., et al., CSrc is necessary for epididymal development and is incorporated into sperm 
during epididymal transit. Developmental Biology, 2012. 369(1): p. 43-53. 
4.  Shum, W.W., et al., Regulation of luminal acidification in the male reproductive tract via cell-
cell crosstalk. J Exp Biol, 2009. 212(Pt 11): p. 1753-61. 
5.  Pietrement, C., et al., Role of NHERF1, Cystic Fibrosis Transmembrane Conductance Regulator, and cAMP in the Regulation of Aquaporin 9. Journal of Biological Chemistry, 2008. 283(5): p. 
6.  Shum, W.W., et al., Epithelial basal cells are distinct from dendritic cells and macrophages in 
the mouse epididymis. Biol Reprod, 2014. 90(5): p. 90. 
7.  Shum,  W.W.,  et  al.,  Transepithelial  projections  from  basal  cells  are  luminal  sensors  in 
pseudostratified epithelia. Cell, 2008. 135(6): p. 1108-17. 
8.  Shum, W.W.C., et al., Regulation of luminal acidification in the male reproductive tract via cell-
cell crosstalk. Journal of Experimental Biology. 212(11): p. 1753-1761. 
9.  Blomqvist, S.R.,  et  al., Epididymal  expression  of  the  forkhead  transcription  factor Foxi1  is 
required for male fertility. EMBO J, 2006. 25(17): p. 4131-41. 
10.  Distribution  of  immune  cells  in  the  epididymis  of  the  aging Brown Norway  rat  is  segment-
specific and related to the luminal content. 1999. 61(3): p. 705-14. 
11.  Hermann,  B.P.,  et  al.,  The  Mammalian  Spermatogenesis  Single-Cell  Transcriptome,  from 
Spermatogonial Stem Cells to Spermatids. Cell Rep, 2018. 25(6): p. 1650-1667 e8. 
12.  Wang,  M. ,  et  al . ,  Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition 
during Human Spermatogenesis. Cell Stem Cell, 2018. 23(4): p. 599-614 e4. 
13.  Kalluri, A.S.,  et  al.,  Single-Cell Analysis  of  the Normal Mouse Aorta  Reveals  Functionally 
Distinct Endothelial Cell Populations. Circulation, 2019. 140(2): p. 147-163. 
14.  Xie, T.,  et  al.,  Single-Cell Deconvolution  of Fibroblast Heterogeneity  in Mouse Pulmonary 
Fibrosis. Cell Rep, 2018. 22(13): p. 3625-3640. 
15.  Guo, J., et al., The adult human testis transcriptional cell atlas. Cell Res, 2018. 28(12): p. 1141-
16.  Rebourcet, D., et al., Sertoli cells control peritubular myoid cell fate and support adult Leydig 
cell development in the prepubertal testis. Development, 2014. 141(10): p. 2139-49. 
17.  Mould,  K.J.,  et  al.,  Single  cell  RNA  sequencing  identifies  unique  inflammatory  airspace 
macrophage subsets. JCI Insight, 2019. 4(5). 
18.  Zimmerman, K.A.,  et  al.,  Single-Cell RNA  Sequencing  Identifies Candidate Renal Resident 
Macrophage Gene Expression Signatures across Species. J Am Soc Nephrol, 2019. 30(5): p. 
19.  DeFalco, T., et al., Macrophages Contribute  to  the Spermatogonial Niche  in  the Adult Testis. 
Cell Rep, 2015. 12(7): p. 1107-19. 
20.  Masaki  and  T.,  Heterogeneity  of  antigen  expression  explains  controversy  over  glomerular 
macrophage accumulation in mouse glomerulonephritis. Nephrology Dialysis Transplantation, 
2003. 18(1): p. 178-181. 
21.  Kalucka,  J., et al., Single-Cell Transcriptome Atlas of Murine Endothelial Cells. Cell, 2020. 
180(4): p. 764-779 e20. 
22.  Lukowski, S.W., et al., Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a 
Hierarchy  from Endovascular Progenitors  to Differentiated Cells. Cell Rep, 2019. 27(9): p. 
2748-2758 e3. 
intermediate monocytes : HLA-DR* [1-5] CD74[6]

naive CD8 T cells : CCR7[7-8],TCF7[8],LEF1[8]

naive CD4 T cells and naive CD8 T cells : CD45RA, CD62L, CD27, CD28, CCR9, CD31 and/or CD103 [9-13]

myeloid DC: CST3, HLA-DPA1, HLA-DQB1[14]

non-classical monocytes:TCF7L2[15,21],MS4A7,MTSS1,CDKN1C[15]

NK:CD56[22], GNLY, NKG7[16]

memory B cell:IGHM [17]

pDC: CD123, CD303, CD304 [22]

mDC(myeloid DC): CD11c, CD13, CD33, CD11b [22]

classical monocytes: CD14, CD11b and CCR2, several S100 calcium binding protein A12 (S100A12), Neuroregulin 1 (NRG1), Phospholipase A Group VII(PLA2G7), cAMP responsive element binding protein 5 (CREB5), A Disintegrin And Metalloproteinase 19 (ADAM19), Low density Lipoprotein Receptor (LDLR), scavenger receptors class B type-1 (SCARB1) and Stabilin-1 (STAB1)[20]

neutrophil-like: S100A8, S100A9, CSF3R [24]


1. Shi J, Fok KL, Dai P, Qiao F, Zhang M, Liu H, Sang M, Ye M, Liu Y, Zhou Y, Wang C, Sun F, Xie G, Chen H. Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq. Cell Discov. 2021 May 18;7(1):34. doi: 10.1038/s41421-021-00260-7. PMID: 34001862; PMCID: PMC8129088.
2. Yang, Jiyeon, et al. “Monocyte and Macrophage Differentiation: Circulation Inflammatory Monocyte as Biomarker for Inflammatory Diseases.” Biomarker Research, vol. 2, Jan. 2014, p. 1. PubMed Central, doi:10.1186/2050-7771-2-1.
Guilliams, Martin, et al. “Developmental and Functional Heterogeneity of Monocytes.” Immunity, vol. 49, no. 4, 16 2018, pp.595–613. PubMed, doi:10.1016/j.immuni.2018.10.005.
3. Günther, Patrick, and Joachim L. Schultze. “Mind the Map: Technology Shapes the Myeloid Cell Space.” Frontiers in Immunology, vol. 10, Oct. 2019. PubMed Central, doi:10.3389/fimmu.2019.02287.
4. Kapellos, Theodore S., et al. “Human Monocyte Subsets and Phenotypes in Major Chronic Inflammatory Diseases.” Frontiers inImmunology, vol. 10, Aug. 2019. PubMed Central, doi:10.3389/fimmu.2019.02035.
CellMarker. 1 Sept. 2020.
5. Zawada AM, Rogacev KS, Rotter B, Winter P, Marell RR, Fliser D, et al.SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset. Blood. (2011) 118:e50–61. doi: 10.1182/blood-2011-01-326827
6. Alanio C, Lemaitre F, Law H K W, et al. Enumeration of human antigen–specific naive CD8+ T cells reveals conserved precursor frequencies[J]. Blood, The Journal of the American Society of Hematology, 2010, 115(18): 3718-3725.
7. Van der Leun A M, Thommen D S, Schumacher T N. CD8+ T cell states in human cancer: insights from single-cell analysis[J]. Nature Reviews Cancer, 2020, 20(4): 218-232.
8. De Rosa, S. C., Herzenberg, L. A., Herzenberg, L. A. and Roederer, M. 2001. 11-color, 13-parameter flow cytometry: identification of human naive T cells by phenotype, function and T-cell receptor diversity. Nat. Med. 7:245.
9. Olaussen, R. W., Farstad, I. N., Brandtzaeg, P. and Rugtveit, J.2001. Age-related changes in CCR9+ circulating lymphocytes: are CCR9+ naive T cells recent thymic emigrants? Scand. J. Immunol.54:435.
10. Kimmig, S., Przybylski, G. K., Schmidt, C. A., Laurisch, K., Mowes,B., Radbruch, A. and Thiel, A. 2002. Two subsets of naive T helper cells with distinct T cell receptor excision circle content in human adult peripheral blood. J. Exp. Med. 195:789.
11. McFarland, R. D., Douek, D. C., Koup, R. A. and Picker, L. J. 2000.Identification of a human recent thymic emigrant phenotype. Proc.Natl Acad. Sci. USA 97:4215.
12. Myeong Sup Lee, Kristina Hanspers, Christopher S. Barker, Abner P. Korn, Joseph M. McCune, Gene expression profiles during human CD4+ T cell differentiation, International Immunology, Volume 16, Issue 8,August 2004, Pages 1109–1124,
13. Wei B, Liu Z, Fan Y, et al. Analysis of Cellular Heterogeneity in Immune Microenvironment of Primary Central Nervous System Lymphoma by Single-Cell Sequencing[J]. Frontiers in oncology, 2021, 11.
14. Hu Y, Hu Y, Xiao Y, et al. Genetic landscape and autoimmunity of monocytes in developing Vogt–Koyanagi–Harada disease[J]. Proceedings of the National Academy of Sciences, 2020, 117(41): 25712-25721.
15. Guo C, Wu M, Huang B, et al. Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19[J]. Genome medicine,2022, 14(1): 1-20.
16. Zhang C, Zhang T X, Liu Y, et al. B-Cell Compartmental Features and Molecular Basis for Therapy in Autoimmune Disease[J].Neurology-Neuroimmunology Neuroinflammation, 2021, 8(6).
17. Psarras A, Antanaviciute A, Alase A, et al. TNF-α regulates human plasmacytoid dendritic cells by suppressing IFN-α production and enhancing T cell activation[J]. The Journal of Immunology, 2021, 206(4): 785-796.
18. Musumeci A, Lutz K, Winheim E, et al. What makes a pDC: Recent advances in understanding plasmacytoid DC development and heterogeneity[J]. Frontiers in immunology, 2019, 10: 1222.
Anbazhagan K, Duroux-Richard I, Jorgensen C, et al. Transcriptomic network support distinct roles of classical and non-classical monocytes in human[J]. International reviews of immunology, 2014,33(6): 470-489.
19. .Schmidl C, Renner K, Peter K, et al. Transcription and enhancer profiling in human monocyte subsets[J]. Blood, The Journal of the American Society of Hematology, 2014, 123(17): e90-e99.
20.Van Acker H H, Capsomidis A, Smits E L, et al. CD56 in the immune system: more than a marker for cytotoxicity?[J]. Frontiers in immunology, 2017, 8: 892.
21.Collin M, McGovern N, Haniffa M. Human dendritic cell subsets[J]. Immunology, 2013, 140(1): 22-30.
22.Kapellos T S, Bonaguro L, Gemünd I, et al. Human monocyte subsets and phenotypes in major chronic inflammatory diseases[J]. Frontiers in immunology, 2019: 2035.

Original code