Notes

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]
Reference 
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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. 
2986-2996. 
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-
1157. 
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. 
767-781. 
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]

References

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CellMarker. http://biocc.hrbmu.edu.cn/CellMarker/search.jsp?quickSearchInfo=monocyte.Accessed 1 Sept. 2020.
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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.
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Original code

https://github.com/broadinstitute/single_cell_classification