The single cell type section - Explore the expression profiles in single cell types

CNN1 - Prostate

TSPY2 - Testis

This section contains Single Cell Type information based on single cell RNA sequencing (scRNAseq) data from 29 human tissues and peripheral blood mononuclear cells (PBMCs). The data is linked to in-house generated immunohistochemically stained tissue sections presented in the Tissue section in order to visualize 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 536 individual cell type clusters corresponding to 15 different cell type groups. A specificity classification was performed to determine the number of genes elevated in these single cell types. 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.

More information about the specific content and the generation and analysis of the data in the section can be found on the Methods Summary.

Learn about:

mRNA and protein expression in single cell types
if a gene is enriched in a particular cell type (specificity)
which genes have a similar expression profile across cell types (expression cluster)

THE SINGLE CELL TYPE PROTEOMESⁱ


Glandular epithelial cells		Squamous epithelial cells
Specialized epithelial cells		Endocrine cells
Neuronal cells		Glial cells
Germ cells		Trophoblast cells
Endothelial cells		Muscle cells
Mesenchymal cells		Adipocytes
Pigment cells	Blood & immune cells	Undifferentiated cells

SINGLE CELL TYPE EXPRESSIONⁱ

The RNA data was used to cluster genes according to their expression across single cell types. The clustering of 19212 genes expressed in single cell types resulted in 77 expression clusters, which have been manually annotated to describe common features in terms of function and specificity. The result of the cluster analysis is presented as a UMAP based on gene expression, where each cluster has been summarized as colored areas containing most of the cluster genes.

Go to interactive expression cluster page

SINGLE CELL TYPE SUMMARYⁱ

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	Enriched	Group enriched	Enhanced	Total elevated
Glandular epithelial cells	Basal respiratory cells	3	18	268	289
	Club cells	2	19	147	168
	Ionocytes	2	33	233	268
	Respiratory ciliated cells	11	132	432	575
	Mucus glandular cells	3	6	144	153
	Serous glandular cells	24	30	160	214
	Gastric mucus-secreting cells	27	47	372	446
	Proximal enterocytes	52	97	722	871
	Paneth cells	7	47	335	389
	Distal enterocytes	5	49	536	590
	Intestinal goblet cells	13	39	291	343
	Exocrine glandular cells	6	33	210	249
	Basal prostatic cells	9	21	175	205
	Prostatic glandular cells	19	20	226	265
	Breast glandular cells	7	10	140	157
	Breast myoepithelial cells	3	13	164	180
	Endometrial ciliated cells	2	127	424	553
	Glandular and luminal cells	3	29	316	348
Squamous epithelial cells	Basal keratinocytes	0	40	262	302
	Suprabasal keratinocytes	60	64	413	537
	Basal squamous epithelial cells	1	29	322	352
	Squamous epithelial cells	1	42	369	412
Specialized epithelial cells	Alveolar cells type 1	7	29	306	342
	Alveolar cells type 2	10	29	193	232
	Salivary duct cells	1	7	118	126
	Ductal cells	1	15	168	184
	Hepatocytes	149	119	575	843
	Cholangiocytes	5	27	176	208
	Proximal tubular cells	32	105	585	722
	Distal tubular cells	13	30	329	372
	Collecting duct cells	9	22	206	237
	Thymic epithelial cells	8	25	222	255
	Sertoli cells	11	30	272	313
	Granulosa cells	14	44	359	417
Endocrine cells	Enteroendocrine cells	18	50	212	280
	Pancreatic endocrine cells	8	29	166	203
	Leydig cells	2	44	293	339
	Theca cells	10	26	203	239
Neuronal cells	Excitatory neurons	23	460	1789	2272
	Inhibitory neurons	25	466	1650	2141
	Cone photoreceptor cells	24	110	518	652
	Rod photoreceptor cells	28	101	636	765
	Bipolar cells	21	100	577	698
	Horizontal cells	11	99	680	790
Glial cells	Astrocytes	35	232	989	1256
	Oligodendrocyte precursor cells	22	349	1262	1633
	Oligodendrocytes	80	227	1318	1625
	Microglial cells	12	148	660	820
	Muller glia cells	21	58	385	464
	Schwann cells	12	28	332	372
Germ cells	Spermatogonia	27	141	397	565
	Spermatocytes	54	367	1017	1438
	Early spermatids	128	1039	1770	2937
	Late spermatids	265	991	1744	3000
Trophoblast cells	Cytotrophoblasts	1	62	357	420
	Syncytiotrophoblasts	53	92	645	790
	Extravillous trophoblasts	28	70	582	680
Endothelial cells	Endothelial cells	4	68	296	368
Muscle cells	Cardiomyocytes	57	106	579	742
	Skeletal myocytes	83	111	316	510
	Smooth muscle cells	4	34	336	374
Adipocytes	Adipocytes	10	72	416	498
Pigment cells	Melanocytes	18	31	209	258
Mesenchymal cells	Fibroblasts	4	45	352	401
	Peritubular cells	2	38	354	394
	Endometrial stromal cells	3	20	258	281
Undifferentiated cells	Undifferentiated cells	3	23	222	248
Blood & immune cells	T-cells	75	104	322	501
	B-cells	14	49	294	357
	Plasma cells	160	58	447	665
	NK-cells	16	80	442	538
	Granulocytes	20	42	285	347
	Monocytes	4	74	610	688
	Macrophages	1	93	418	512
	Hofbauer cells	10	92	448	550
	Kupffer cells	4	88	360	452
	Dendritic cells	13	33	430	476
	Langerhans cells	16	51	558	625
	Erythroid cells	40	37	366	443