根据平时的文献阅读，汇总前人注释单细胞数据的细胞类型所使用的marker gene，以供后续研究参考。（持续更新）

1、Tumor

  • B cell：CD79A*[1-3]，CD79B[1,3]，CD19[1,3]，MS4A1[2,3]，IGKC[1]，MZB1[2]*

  • T cell：CD3C*[1,2]，CD3E[1,2]，TRAG[1]，CD3G[1]，CD2[2]*

  • Epithelial(Tumor) cell：EPCAM*[1,3]，KRT18[1,3]，CD24[1,2]，KRT19[1,3]，PAX8[1]，SCGB2A2[2]，KRT5[3]，KRT15[3]*

  • Fibroblast(CAF)：COL1A1*[1-3]，DCN[1-3]，COL1A2[1]，COL3A1[3]，BGN[1]，POSTN[1]，C1R[2]*

  • Meyloid cell：CD68*[1-3]，LYZ[1-3]，MARCO[1]，AIF1[1]，TYROBP[2]，MS4A6A[3]，CD1E[3]，IL3RA[3]，LAMP3[3]*

  • NK cell：NCR1*[1]，NCAM[1]，KLRC1[1]，KLRC3[1]*

  • Endothelial cell：CLDN5*[1,2]，PECAM1[1]，VWF[1]，FLT1[2]，RAMP2[2]*

  • Mast cell：CPA3*[1,2]，CMA1[1]，MS4A2[1]，TPSAB1[2]，TPSB2[2]*

[1] High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification（DOI: 10.1186/s13073-021-00922-x）34238352

[2] A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer（DOI: 10.1038/s41591-021-01323-8） 33958794

[3] Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma（DOI: 10.1038/s41422-020-0374-x） 32686767

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## PBMC
genes_to_check = c('CD3D', 'CD3E', 'CD3G', # T cell
				   'CD4','CD8A','CD8B',    # CD4 /CD8
				   'GZMB', 'GZMK','PRF1', # cytotoxicity
				   'CD19', 'CD79A', 'MS4A1', # B cell
                   'CD68', 'CD163', 'CD14', #Monocytes and macrophages
                   'S100A9', 'S100A8', 'MMP19',# monocyte
                   'KLRB1','NCR1', # NK 
				   'MZB1'  # Plasma cells 
				   )

2、Brain

  • Neuron：SYT1*[1]，SNAP25[1]，GRIN1[1]*
    • Excitatory：SLC17A7*[1]，CAMK2A[1]，NRGN[1]*
    • Inhibitory：GAD1*[1]，GAD2[1]*
  • Microglia：CD74*[1]，CSF1R[1]，C3[1]*
  • Astroglia：AQP4*[1]、GFAP[1]*
  • Oligodendrocyte：MBP*[1]，MOBP[1]，PLP1[1]*
  • Endothelial：FLT1*[1]，CLDN5[1]*

[1] Single-cell transcriptomic analysis of Alzheimer’s disease（DOI: 10.1038/s41586-019-1195-2）

3、Bowel Immune

Paper ：The landscape of immune dysregulation in Crohn’s disease revealed through single-cell transcriptomic profiling in the ileum and colon

DOI ：https://doi.org/10.1016/j.immuni.2023.01.002

（1）Epithelial ：EPCAM, KRT8, KRT18

  • Enterocyte肠上皮：RBP2, ANPEP,FABP2
  • Stem cell：LGR5, ASCL2, SMOC2, RGMB, OLFM4
  • Goblet cell 杯状细胞：CLCA1, SPDEF, FCGBP, ZG16, MUC2
  • Paneth cell 潘氏细胞：DEFA5,DEFA6, REG3A
  • Tuft cell 簇细胞：LRMP, SH2D6
  • Enteroendocrine cell肠内分泌细胞：CHGA, CHGB, NEUROD1
  • Cycling ：UBE2C, TOP2A, MKI67, HMGB2

（2）Stromal ：CDH5, COL1A1, COL1A2, COL6A2, VWF

  • Fibroblast成纤维细胞：ADAMDEC1, PDGFRA, BMP4
  • Myofibroblasts成肌纤维细胞：TAGLN, ACTG2
  • Lymphatics淋巴：CCL21, TFF3
  • Endothelial cell ：CD36, DARC/ACKR1
  • Pericyte周皮细胞：NOTCH3, MCAM/CD146, RGS5
  • Glial cell：FOXD3, MPZ, CDH19, PLP1, SOX10, S100B, ERBB3

（3）Immune：CD45/PTPRC, CD3D, CD3G, CD3E, CD79A, CD79B, CD14, CD16, CD68, CD83, CSF1R, FCER1G

  • T cell ：CD3D, CD3G, CD3E
    • CD8 T ：CD8A, CD8B
    • CD4 T ：CD4
    • Innate lymphoid cells (ILCs)先天性淋巴样细胞：RORC, IL1R1, IL23R, KIT, TNFSF4, PCDH9
    • NK：EOMES, PRF1, NKG7
  • B cell ： CD79A, MS4A1/CD20, CD19
    • Plasma cell ：SDC1, MZB1, SSR4, XBP1
    • B cell ：BANK, MS4A1/CD30, ADAM28, VPREB3
    • Germinal Center (GC) 生发中心B cell ：LRMP, GPT2, PAG1
  • Myeloid ：CD14, CD16, HLA-DR
    • Mast cell ：GATA2, CPA3, HPGDS
    • classical Macrophages：CD163, C1QB, C1QC
    • classical Monocytes：FCN1, S100A4, S100A6
    • dendritic cell，DC1 ：CLEC9A, XCR1
    • dendritic cell，DC2 ： CLEC10A, FCER1A