Cell type Annotation

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  • Annotation Immune cell types using scType (scRNA-seq)
  • scType link

scType application

suppressPackageStartupMessages(invisible(lapply(c("dplyr", "Seurat", "HGNChelper", "openxlsx"), library, character.only = TRUE)))


# load gene set preparation function
source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/gene_sets_prepare.R")
# load cell type annotation function
source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/sctype_score_.R")


# DB file (Human)
db_ <- "https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/ScTypeDB_full.xlsx";
tissue <- "Immune system" # e.g. Immune system,Pancreas,Liver,Eye,Kidney,Brain,Lung,Adrenal,Heart,Intestine,Muscle,Placenta,Spleen,Stomach,Thymus 

# prepare gene sets
gs_list <- gene_sets_prepare(db_, tissue)

# extract scaled scRNA-seq matrix
scRNAseqData_scaled <- as.matrix(obj.srt[["RNA"]]@scale.data)

# run ScType
es.max <- sctype_score(scRNAseqData = scRNAseqData_scaled, 
                       scaled = TRUE, 
                       gs = gs_list$gs_positive, 
                       gs2 = gs_list$gs_negative)
url <- "https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/ScTypeDB_full.xlsx"
temp_file <- tempfile(fileext = ".xlsx")
download.file(url, temp_file, mode = "wb", quiet = TRUE) 

# Read excel file 
sheets <- openxlsx::getSheetNames(temp_file)
data_list <- lapply(sheets, function(sheet) openxlsx::read.xlsx(temp_file, sheet = sheet))

# The first sheet includes the information 
table_data <- data_list[[1]][data_list[[1]]$tissueType == "Immune system",c(1,2,5,3)]

Cluster annotaion (res 0.2)

Annotaion report

# Merge by cluster

# Select resolution
res <- paste0("RNA_snn_res.", 0.2)

# Annotation report 
if (res %in% colnames(obj.srt@meta.data)) {
  cL_results <- do.call("rbind", 
                        lapply(unique(obj.srt@meta.data[, res]), function(cl) {
                          cl_data <- obj.srt@meta.data[obj.srt@meta.data[, res] == cl, ]
                          es_sum <- rowSums(es.max[, rownames(cl_data)])
                          es_sorted <- sort(es_sum, decreasing = TRUE)
                          top_es <- head(data.frame(cluster = cl, 
                                                    type = names(es_sorted), 
                                                    scores = es_sorted, 
                                                    ncells = nrow(cl_data)), 10)
                          return(top_es)
                        })
  )
} else {
  stop(paste("Column", res, "not found in obj.srt@meta.data"))
}

Table

Heatmap

Suggested Cell type

Cluster annotaion (res 0.4)

Annotaion report

# Merge by cluster

# Select resolution
res <- paste0("RNA_snn_res.", 0.4)

# Annotation report 
if (res %in% colnames(obj.srt@meta.data)) {
  cL_results <- do.call("rbind", 
                        lapply(unique(obj.srt@meta.data[, res]), function(cl) {
                          cl_data <- obj.srt@meta.data[obj.srt@meta.data[, res] == cl, ]
                          es_sum <- rowSums(es.max[, rownames(cl_data)])
                          es_sorted <- sort(es_sum, decreasing = TRUE)
                          top_es <- head(data.frame(cluster = cl, 
                                                    type = names(es_sorted), 
                                                    scores = es_sorted, 
                                                    ncells = nrow(cl_data)), 10)
                          return(top_es)
                        })
  )
} else {
  stop(paste("Column", res, "not found in obj.srt@meta.data"))
}

Table

Heatmap

Suggested Cell type

scType DB full list

download

ScTypeDB
tissueType cellName shortName geneSymbolmore1
1 Immune system Pro-B cells Pro-B CD27,IgD,CD24,PTPRC,PAX5,CD24,CD38,CD79A,DNTT,C10orf10,VPREB1,ARPP21,CD99,IGLL1,CD9,CD79B,TCL1A,IGLL5,HLA-DQA1,HLA-DQB1,VPREB3,IGLL5
2 Immune system Pre-B cells Pre-B CD19,CD27,IgD,CD24,PTPRC,PAX5,CD24,CD38,CD79A,NSMCE1,PCDH9,ACSM3,CCDC191,TCL1A,CD79B,TCL1A,IGLL5,HLA-DQA1,HLA-DQB1,VPREB3,IGLL5
3 Immune system Naive B cells Naive B CD19,IgD,CD38,CD24,CD20,MS4A1,PTPRC,PAX5,CD24,CD38,CD79A,JCHAIN,SSR4,FKBP11,SEC11C,DERL3,PRDX4,IGLL5,CD79B,TCL1A,IGLL5,HLA-DQA1,HLA-DQB1,CD138,CD38,VPREB3,IGLL5
4 Immune system Memory B cells Memory B CD19,CD27,IgD,CD38,CD24,CD20,MS4A1,PTPRC,PAX5,CD24,CD38,CD79A,JCHAIN,SSR4,FKBP11,SEC11C,DERL3,PRDX4,IGLL5,CD79B,TCL1A,IGLL5,HLA-DQA1,HLA-DQB1,CD138,CD38,CD27,VPREB3,IGLL5
5 Immune system Plasma B cells Plasma B CD27,IgD,CD38,CD24,CD20,MS4A1,PTPRC,PAX5,CD24,CD38,CD79A,JCHAIN,SSR4,FKBP11,SEC11C,DERL3,PRDX4,IGLL5,CD79B,TCL1A,IGLL5,HLA-DQA1,HLA-DQB1,CD138,CD38,VPREB3,IGLL5
6 Immune system Naive CD8+ T cells Naive CD8+ T CD8,CD2,CD3D,CD3E,CD3G,CD3Z,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CD8A,CD8B,CCR6,CD11b,CD30,CD6,CTLA4,IL2RA,GZMB,PTPRC,SELL,CCR7,GNLY,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
7 Immune system Naive CD4+ T cells Naive CD4+ T CD4,CD2,CD3D,CD3E,CD3G,CD3Z,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CCR6,CD11b,CD30,CD6,CTLA4,IL2RA,GZMB,PTPRC,SELL,CCR7,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
8 Immune system Memory CD8+ T cells Memory CD8+ T CD8,CD2,CD3D,CD3E,CD3G,CD3Z,CD25,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CD8A,CD8B,CCR6,CD11b,CD30,CD45RO,CD6,CTLA4,IL2RA,GZMB,SELL,CCR7,GNLY,S100A4,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
9 Immune system Memory CD4+ T cells Memory CD4+ T CD4,CD2,CD3D,CD3E,CD3G,CD3Z,CD25,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CCR6,CD11b,CD30,CD45RO,CD6,CTLA4,IL2RA,GZMB,SELL,CCR7,S100A4,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
10 Immune system Effector CD8+ T cells Effector CD8+ T CD8,CD2,CD3D,CD3E,CD3G,CD3Z,CD25,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CD8A,CD8B,CCR6,CD11b,CD30,CD6,CTLA4,IL2RA,GZMB,PTPRC,GNLY,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
11 Immune system Effector CD4+ T cells Effector CD4+ T CD4,CD2,CD3D,CD3E,CD3G,CD3Z,CD25,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CCR6,CD11b,CD30,CD6,CTLA4,IL2RA,GZMB,PTPRC,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
12 Immune system γδ-T cells γδ-T CD2,CD3D,CD3E,CD3G,CD3Z,CD25,CD45RA,CD62L,CD27,CD127,FOXP3,CCR7,CD45,CCR6,CD11b,CD30,CD6,CTLA4,IL2RA,GZMB,PTPRC,TRDV2,TRGV9,TRGC1,Trac,Ltb,Cd52,Trbc2,Shisa5,Lck,Thy1,Dapl1
13 Immune system Platelets Platelets CD41,CD42b,CD61,CD31,PPBP,PF4,GNG11,SDPR,CLU,CD41,CD110
14 Immune system CD8+ NKT-like cells CD8+ NKT CD8,CD56,CD2,CD16,CD94,CD3D,CD3E,CD3G,CD3Z,NKp46,CD11b,CD161,CD314,CD69,NKG7,CD122,NKG2D,GZMB,GZMA,GZMM,GNLY,COX6A2,ZMAT4,KIR2DL4
15 Immune system CD4+ NKT-like cells CD4+ NKT CD4,CD56,CD2,CD16,CD94,CD3D,CD3E,CD3G,CD3Z,NKp46,CD11b,CD161,CD314,CD69,NKG7,CD122,NKG2D,GZMB,GZMA,GZMM,COX6A2,ZMAT4,KIR2DL4
16 Immune system Natural killer cells NK CD56,CD2,CD16,CD94,NKp46,CD11b,CD161,CD314,CD69,NKG7,CD122,NKG2D,GZMB,GZMA,GZMM,FCGR3A,GNLY,COX6A2,ZMAT4,KIR2DL4,NKG7
17 Immune system Eosinophils Eosinophils CD11b,CD193,CD123,CD125,CD15,SIGLEC8,CLC,GATA1,CEBPE,SEMG1,ALOX15,CCL23,PRSS41,PRSS33,THBS4,FOXI1
18 Immune system Neutrophils Neutrophils CD66b,CD11b,CD15,CD16,CXCL8,FCGR3B,MNDA,CXCR2,MPO,ELANE,PRTN3,MPO,AZU1,LYZ,S100A8,S100A9,PI3,CHI3L1,ANXA3,CXCL1,TGM3,BTNL3,C4BPA,MMP9,CD24,BPI,LTF,GCA,Camp,Ngp,Chil3,Ltf
19 Immune system Basophils Basophils CD63,CD203c,CD123,CLC,MS4A3,TCN1,CPA3,HDC,GATA2,MS4A2,IL4,GCSAML,GATA2,TPSAB1
20 Immune system Mast cells Mast CD117,CD203c,CD25,KIT,SLC18A2,CD33,CD32,FCER1A,TPSD1,HPGDS
21 Immune system Classical Monocytes C_Monocytes CD14,CD11b,CD68,HLA-DR,CD33,CD11c,CD123,CD15,CD3D,CD3E,CD3G,CD3Z,CD66b,VCAN,S100A12,CXCL8,S100A8,S100A9,LYZ,CST3,Elane1
22 Immune system Non-classical monocytes N_Monocytes CD14,CD16,CD11b,CD68,HLA-DR,CD33,CD11c,CD123,CD15,CD3D,CD3E,CD3G,CD3Z,CD66b,FCGR3A,CDKN1C,LST1,FCER1G,MS4A7,RHOC,S100A8,S100A9,CST3,C1QC,Elane1
23 Immune system Intermediate monocytes I_Monocytes CD14,CD16,CD11b,CD68,HLA-DR,CD33,CD11c,CD123,CD15,CD3D,CD3E,CD3G,CD3Z,CD66b,IL1B,S100A8,S100A9,CST3,C1QC,Elane1
24 Immune system Macrophages MΦ CD68,CD163,CD14,CD11b,CD206,CD80,CD86,CD16,CD64,CCL18,CD115,CD11c,CD32,HLA-DR,MRC1,MSR1,GCA,Pf4
25 Immune system Megakaryocyte MKs CD61,CD41,CD42b,CD41a,CD42a,CXCR4,CD110
26 Immune system Endothelial ECs PECAM1,CD34,KDR,CDH5,PROM1,PDPN,TEK,FLT1,VCAM1,PTPRC,VWF,ENG,MCAM,ICAM1,FLT4,SELE
27 Immune system Erythroid-like and erythroid precursor cells Es PTPRC,GYPA,RUVBL1,TFRC,FOLR1,CD36,ITGA4,HBB,CD235a,HBD,CA1
28 Immune system HSC/MPP cells HSC/MPP CD105,CD34,CD44,CD73,CD45,CD29,STRO-1,NANOG,SOX2,CD133,CD166,CD146,CD31,Nestin,OCT4,CD117,KDR,CXCL8,AVP,CRHBP,ALDH1A1,CD49,CD90,CD69,CD24,CD38,CD45RA,Keratin-19,ASPM,CD10,CD123,ABCG2,CD135,CD49f,EpCAM,Keratin-7,SCA-1,CD14,CD150,CD271,HLA-DR
29 Immune system Progenitor cells PCs CD105,CD34,CD44,CD73,CD45,CD29,STRO-1,NANOG,SOX2,CD133,CD166,CD146,CD31,Nestin,OCT4,CD117,KDR,AVP,CRHBP,ALDH1A1,STMN1,CD38,PTPRC,CD135
30 Immune system Myeloid Dendritic cells mDCs ITGAX,CD83,CD1C,NRP1,CLEC4C,CD86,IL3RA,CD80,CD1A,ITGAX,CD40,HLA-DQA1,CD11c,HLA-DR,HLA-DPB1,HLA-DPA1,CLEC10A,CST3,GPR31,ODF3L1,PRB2,CD207,ARSE,CLEC141,MRC,EBLN1,CRIP3
31 Immune system Plasmacytoid Dendritic cells pDCs ITGAX,CD83,CD1C,NRP1,CLEC4C,CD86,IL3RA,CD80,CD1A,ITGAX,CD40,HLA-DQA1,CD11c,HLA-DR,HLA-DPB1,HLA-DPA1,CLEC10A,CST3,TPM2,LRRC26,ASIP,GPM6B,KRT5,NTM,SCT,SHD,KCNA5,SCARA5,EPHA2,MYMX
32 Immune system Granulocytes Gs CD203c,CD15,CD11b,CD63,CD66b,CD123,CD16,CD33,CD117,CD45,Fc-epsilon RI-alpha,CD125,CD13,CD14,CD25,CD44,CD69,CD9,HLA-DR,CCR3,CD116,CD11c,CD193,CD24,CD32,CD43,CXCL8,FCGR3B,MNDA,SIGLEC8,AZU1,MPO,CTSG,LYZ
33 Immune system ISG expressing immune cells ISG+ IFIT1,IFIT2,IFIT3,IFIT5,ISG15,CCL3,CCL4,CCL3L3,RSAD2,OASL,CXCL10,IFI15,ISG20
234 Immune system Cancer cells Cancer CD44,EPCAM,ERBB2,FOLH1,KRT18,PROM1