The Single Cell Type Atlas

CNN1 - Prostate

TSPY2 - Testis

The Single Cell Type Atlas contains single cell RNA sequencing (scRNAseq) data from 13 different human tissues, together with in-house generated immunohistochemically stained tissue sections visualizing the corresponding spatial protein expression patterns. The scRNAseq analysis was based on publicly available genome-wide expression data and comprises all protein-coding genes in 192 individual cell type clusters corresponding to 12 different cell type groups. A specificity and distribution classification was performed to determine the number of genes elevated in these single cell types, and the number of genes detected in one, several or all cell types, respectively. The genes expressed in each of the cell types can be explored in interactive UMAP plots and bar charts, with links to corresponding immunohistochemical stainings in human tissues.


Classification of all protein-coding genes based on single cell type-specific expression, determining the number of genes elevated (cell type/group enriched, cell type enhanced) in a particular cell type compared to all other cell types.

Cell type group Cell type EnrichedGroup
Epithelial cells Enterocytes 1274518604
Mucus-secreting cells 1454268336
Paneth cells 970333412
Ciliated cells 1162897531158
Club cells 9174392575
Exocrine glandular cells 2944274347
Basal glandular cells 136236273
Glandular cells 935189233
Basal keratinocytes 672345423
Suprabasal keratinocytes 3887380505
Cholangiocytes 1346251310
Hepatocytes 191147543881
Alveolar cells type 1 26130496652
Alveolar cells type 2 24167453644
Collecting duct cells 2895381504
Distal tubular cells 3887520645
Proximal tubular cells 58135551744
Ductal cells 533191229
Sertoli cells 19100405524
Urothelial cells 1154378443
Endocrine cells Intestinal endocrine cells 4685314445
Pancreatic endocrine cells 1552336403
Leydig cells 10115341466
Neuronal cells Cone photoreceptor cells 322328691133
Rod photoreceptor cells 27219697943
Bipolar cells 55235702992
Horizontal cells 73192726991
Glial cells Muller glia cells 69169509747
Germ cells Spermatogonia 54155448657
Spermatocytes 653108101185
Early spermatids 231131116163158
Late spermatids 61118512862532
Trophoblast cells Cytotrophoblasts 296353451
Syncytiotrophoblasts 59137564760
Extravillous trophoblasts 31113504648
Vascular cells Endothelial cells 273181256
Muscle cells Cardiomyocytes 179139562880
Smooth muscle cells 566278349
Pigment cells Melanocytes 3685273394
Mesenchymal cells Fibroblasts 353186242
Ito cells 30113409552
Peritubular cells 9130424563
Undifferentiated cells Undifferentiated cells 237166205
Blood & immune cells B-cells 2263170255
T-cells 5485241380
Granulocytes 39161376576
Monocytes 4966481596
Macrophages 4123280407
Hofbauer cells 26146488660
Kupffer cells 13137465615
Erythroid cells 4645258349