| 细胞类型 | marker基因 |
|---|---|
| T Cells | CD3D, CD3E |
| Th | CD3D, CD3E, CD40LG |
| Tc | CD3D, CD3E, CD8A, CD8B |
| gdT | TRDV2, TRGV9 |
| B cells | CD19, CD79A, CD79B, MS4A1 [CD20] |
| Plasma cells | IGHG1, MZB1, SDC1, CD79A |
| Monocytes and DCs | CST3, LYZ |
| Monocytes and macrophages | CST3, LYZ, CD68, CD163, CD14 |
| NK Cells | FGFBP2, FCG3RA, CX3CR1, GNLY, NKG7, TYOBP, PRF1 |
| Neutrophils | CST3, LYZ, FCGR3B, CSF3R |
| Photoreceptor cells | RCVRN |
| Megakaryocytes | CST3, PF4, PPBP |
| Fibroblasts | FGF7, MME |
| Endothelial cells | PECAM1, VWF |
| epi or tumor | EPCAM, KRT18, KRT19, PROM1, ALDH1A1, CD24 |
| immune | CD45,PTPRC |
| epithelial/cancer | EpCAM+,EPCAM |
| stromal | CD10+,MME,fibo or CD31+,PECAM1,endo |
| mast cell | CST3, KIT, CPA3 |
| RBC | HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, HBZ（用于细胞过滤） |
文献：dropClust: efficient clustering of ultra-large scRNA-seq data
| Potential cell type | Markers |
|---|---|
| Naive T cells | CD27, CCR7, CD8A, CD8B |
| CD4+ memory cells | IL7R, CD27, CCR7 |
| NKT cells | ZNF683, CD8A, CD8B |
| B cells | CD79A, CD37 |
| CD8+ T cells | GZMK, CD8A, CD8B |
| NK cells | CD160, NKG7, GNLY, CD247, CCL3, GZMB |
| CD16+ and CD14+ monocytes | CD68, CD16(FCGR3A), CD14, S100A12 |
| Regulatory T cells | CCR10, CD25(IL2RA), CD52, CMTM7, FOXP3 |
| Monocyte derived dendritic cells | CST3, CD1C, FCER1A |
| Megakaryocyte progenitors | PF4, PPBP, PLA2G12A |
| Progenitor-NK cells | ID2 |
| Plasmacytoid dendritic cells | GZMB, CD123(IL3RA) |
library(ggplot2)
genes_to_check = c('PTPRC', 'CD3D', 'CD3E', 'CD8A','CD19', 'CD79A', 'MS4A1' ,
'IGHG1', 'MZB1', 'SDC1',
'CD68', 'CD163', 'CD14',
'RCVRN',
'FGF7','MME',
'PECAM1', 'VWF',
'EPCAM' , 'KRT19', 'PROM1', 'ALDH1A1' )
library(stringr)
p <- DotPlot(sce.all, features = genes_to_check,
assay='RNA' ) + coord_flip()
p
ggsave(plot=p, filename="check_marker_by_seurat_cluster.pdf")
张泽民老师的文章里对各类细胞的注释极为详细，可以参考。
出自Single-Cell Analyses Inform Mechanisms of Myeloid- Targeted Therapies in Colon Cancer
出自COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas
亚群细分时不必拘泥于现有分类，可以使用marker基因来对细胞群命名，后续查看这些细胞群是否有生物学意义。
PBMC的注释：
文献：Temporally integrated single cell RNA sequencing analysis of PBMC from experimental and natural primary human DENV-1 infections
文献：A single-cell map for the transcriptomic signatures of peripheral blood mononuclear cells in end-stage renal disease
文献：Single-cell RNA sequencing reveals the sustained immune cell dysfunction in the pathogenesis of sepsis secondary to bacterial pneumonia
- 先分大群
T/NK cells (CD3D+ IL32+ NKG7+), myeloid cells (CD14+ FCGR3A+ S100A9+) and B cells (CD79B+ CD79A+ IGHM+)
- 再细分亚群
