The Blood Atlas




The Blood Atlas contains single cell type information on genome-wide RNA expression profiles of human protein-coding genes covering various B- and T-cells, monocytes, granulocytes and dendritic cells. The single cell transcriptomics analysis covers 18 cell types isolated with cell sorting followed by RNA-seq analysis. In addition, an analysis of the “human secretome” is presented including annotation of the genes predicted to be actively secreted to human blood, as well as the annotation of proteins predicted to be secreted to other parts of the human body, such as the gastric tract and local compartments. An analysis of the proteins detected in human blood is also presented with an estimation of the respective protein concentrations determined either with mass spectrometry-based proteomics or antibody-based immune assays.

Hematopoietic Stem Cell Common Lymphoid Progenitor Common Myeloid Progenitor Mastcells Myeloblasts Erythrocytes Platelets Lymphocytes NK-cells B-cells T-cells Granulocytes Monocytes Dendritic Cells
Classical monocyte
Intermediate monocyte
Non-classical monocyte
Myeloid DC
Plasmacytoid DC
Memory B-cell
Naive B-cell
MAIT T-cell
Memory CD4 T-cell
Memory CD8 T-cell
Naive CD4 T-cell
Naive CD8 T-cell

The genome-wide RNA expression profiles of human protein-coding genes in 18 single cell types are presented covering various B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells. The RNA expression for each gene with a classification based on the RNA expression of individual cell types across the 18 cell types is presented as well as a classification based on the main cell lineage types. This classification is based on the same principal used for the tissue-based classification resulting in the annotation of each gene according to cell type specificity (cell type enriched, group enriched, cell type enhanced and low cell type specificity) and cell type distribution (detected in single, few, many or all cell types). The cell type specific protein-coding genes are high-lighted and genome-wide differential analysis of the expression profiles between the different cell lineages and cell types are presented.

Figure 1: Example of two categories of blood cell lineage-elevated genes. The number of cell lineage-elevated genes with highest expression in blood or lymphoid tissues to the left and the cell lineage-enriched genes with highest expression in blood or lymphoid tissues to the right. All blood cell specific categories can be found here.


The proteins secreted by human tissues (the secretome) are important for the basic understanding of human biology, but also for identification of potential targets for future diagnostics and therapy. Based on a genome-wide analysis of the human protein-coding genes in which the secretome was identified as proteins with a signal peptide and no transmembrane-spanning region altogether 2641 genes were identified, corresponding to approximately 13% of the protein-coding genes. We have here performed a systematic analysis of all of these genes in order to identify through litterature, bioinfomatics and experimental data the final location of each of these predicted secreted proteins with the aim to annotate their final location in the human body, including blood, digestive tract or other locations. Each gene was annotated with a single location and the categories and their mutual order was Intracellular and membrane, Secreted to blood, Secreted in brain, Secreted to digestive system, Secreted in female reproductive system, Secreted in male reproductive system, Secreted to extracellular matrix, Secreted in other tissues, Secreted - unknown location. A large portion of the proteins were annotated as intracellular, including locations in the Golgi, ER and other intracellular compartments. Below the genes annotated to each of these compartments are displayed and the complete list can be obtained by clicking the relevant icon.

The human secretome

Secreted to extracellular matrix

Secreted to blood

Secreted in other tissues

Secreted in brain

Secreted - unknown location

Secreted to digestive system

Secreted in male reproductive system

Intracellular and membrane

Secreted in female reproductive system


Here, we present the estimated protein concentrations of proteins detected in human plasma based on immunoassays and mass spectrometry-based proteomics, respectively.

Proteins detected
by immmunoasay

Proteins detected
by MS

Proteins detected
by PEA