The Single Cell Resource

The Single Cell resource of the Human Protein Atlas presents comprehensive data on gene expression across various human tissues and cell types, utilizing single cell RNA sequencing (scRNAseq), cell sorting, single nuclei RNA sequencing (snRNAseq), and bulk RNAseq correlation analyses. The resource provides insights into mRNA and protein expression patterns, gene specificity, and expression clustering with single cell types, immune cells and brain single nuclei. The Single Cell Resource includes four main datasets:

  • The Single cell type section, providing the expression profiles across 81 cell types from 31 human tissues, and cell type specificity based on gene expression.
  • The Tissue cell type section, providing the predicted cell-type expression specificity based on bulk RNAseq
  • The Single nuclei brain section, providing more details regarding cell type specificity within the brain, based on single nuclei RNAseq
  • The Immune cell section, providing expression comparison between sorted immune cells

Learn more about each of these four parts down below, and explore the details of each dataset, or serach for a gene and browse the expression details side by side across the different datasets on the gene summary pages. More information about the content, the generation and analysis of the data in this resource can be found under respective link or here for single cell type, tissue cell type, single nuclei brain and immune cell. Additionally, each focused section is based on different datasets, see more details here for single cell type, tissue cell type (using GTEx RNAseq data), single nuclei brain and immune cell.

Single cell type

Providing the mRNA expression profiles of protein-coding genes from 31 human tissues including peripheral blood mononuclear cells (PBMCs) across single cell types. The scRNAseq analysis is based on publicly available genome-wide expression data and comprises all protein-coding genes in 557 individual cell type clusters corresponding to 15 different cell type groups and 81 individual cell types.


05001,0001,5002,000nTPM
MYH2 - Skeletal muscle

Tissue cell type

Providing cell type expression specificity predictions for all human protein-coding genes within 18 different tissue types, generated using correlation-based integrated network analysis of publicly available bulk RNAseq data.

0.30.40.50.60.70.80.91.0Enrichment
DCD - Skin

Single nuclei brain

Providing the mRNA expression profiles of protein-coding genes in cluster cell types across 11 different brain regions. The snRNAseq analysis is based on publicly available genome-wide expression data from over 2,5 milion brain cells, described by 34 cluster cell types, representing the cell of the brain.


02004006008001,000nTPM
HAPLN2 - Spinal cord

Immune cell

Providing the expression profiles of protein-coding genes in human immune cells based on flow-sorted cells from blood, covering 18 cell types grouped into 6 immune cell lineages. The transcriptomic data includes classification based on specificity, distribution and expression clusters across the different immune cells.

BasophilEosinophilNeutrophilClassical monocyteNon-classical monocyteIntermediate monocyteT-regGdT-cellMAIT T-cellMemory CD4 T-cellNaive CD4 T-cellMemory CD8 T-cellNaive CD8 T-cellMemory B-cellNaive B-cellPlasmacytoid DCMyeloid DCNK-cellTotal PBMC05001,0001,5002,000
CD3D

Transcription factor landscape

Explore the expression landscape of the 1485 transcription factors throughout human cell types representing both normal tissue and cell types, as well as cancer cell lines.


The tissue and cell specific proteome

Explore the genes with elevated expression profiles in different cell and tissue types, and how they overlap. Find easy clickable seach functions and examples verified at protein level using immunohistochemistry.