Atlas of Human Blood Cells

UMAP displays of the 7,551 human blood cells

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Filtered criterion: fold-change ≥ 2 & adjusted P-value ≤ 0.05
Download Marker Genes Information

Hematopoietic hierarchy deduced by regulons

20 regulatory clusters

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Filtered criterion: fold-change ≥ 2 & adjusted P-value ≤ 0.05
Download TF Information

Transcriptional atlas of 7,192 cells based on lncRNAs

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Filtered criterion: fold-change ≥ 2 & adjusted P-value ≤ 0.05
Download lncRNAs Information

Elaborate atlas for 8 hematopoietic cell population based on RNA

HSPC

1,909 cells , 12 clusters

HSPC

1,909 cells , 12 clusters

B

1,448 cells , 7 clusters

B

1,448 cells , 7 clusters

NK

532 cells , 4 clusters

NK

532 cells , 4 clusters

CD4T

246 cells , 3 clusters

CD4T

246 cells , 3 clusters

CD8T

271 cells , 3 clusters

CD8T

271 cells , 3 clusters

Monocyte

940 cells , 6 clusters

Monocyte

940 cells , 6 clusters

Neutrophil

458 cells , 3 clusters

Neutrophil

458 cells , 3 clusters

Erythrocyte

1,747 cells , 5 clusters

Erythrocyte

1,747 cells , 5 clusters

Elaborate atlas for 8 hematopoietic cell population based on lncRNAs

HSPC

1,845 cells , 11 clusters

HSPC

1,845 cells , 11 clusters

B

1,390 cells , 7 clusters

B

1,390 cells , 7 clusters

NK

498 cells , 4 clusters

NK

498 cells , 4 clusters

CD4T

241 cells , 3 clusters

CD4T

241 cells , 3 clusters

CD8T

258 cells , 3 clusters

CD8T

258 cells , 3 clusters

Monocyte

929 cells , 6 clusters

Monocyte

929 cells , 6 clusters

Neutrophil

413 cells , 3 clusters

Neutrophil

413 cells , 3 clusters

Erythrocyte

1,526 cells , 5 clusters

Erythrocyte

1,526 cells , 5 clusters

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Cell Prediction

Original Atlas

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Download prediction result Download example input

Gene expression matrix

Matrix file contains the single-cell expression data of our 7,551 cells in scRNA-seq.

Download matrix

Cell metadata

A tab-delimited file contains RNA clusters, immunophenotypes and tissues of each cell.

Download metadata

Transcription Factor

A tab-delimited file contains specific sets of active regulons in 20 regulatory clusters.

Marker information

A tab-delimited file contains the signature genes in 43 transcriptional cell clusters.

Download marker

LncRNA information

A tab-delimited file contains signature lncRNAs for 42 clusters of 7,192 human blood cells.

Download LncRNAs

Home

7,551 human blood cells were profiled using single-cell RNA-seq (STRT-seq), covering 32 immunophenotypic cell types from 21 healthy donors. An average 3,079 protein-coding genes and 1,714 lncRNAs were detected per single cell by deep sequencing respectively.
The detailed antibodies for each cell type, along with the number of donors and single cells for each population are shown in the figure below.

The interface displays 4 modules:
Marker Gene: Information of 43 transcriptional cell clusters and signature genes with AUC score.
Transcription Factor: Hematopoietic cells were grouped into 20 regulatory clusters, termed as C1 to C20 hereafter, and each showed activations of highly specific sets of regulons.
LncRNA: We constructed the transcriptional atlas of 7,192 human blood cells based on lncRNAs. The signature lncRNAs for 42 clusters were dispalyed.
Trajectory: UMAP displays of the transcriptional clusters by seurat and differentiation trajectory by monocle3 for HSPCs, erythrocytes, B cells, NK cells, CD4T cells, CD8T cells, monocytes and neutrophils. Colors correspond to cell clusters.

Browser

The interface is to help search the gene expression of any given gene in single cells grouped by 43 transcriptional clusters or 32 immunophenotypic cell types, and displayed via boxplot.

Usage:
1. Enter a gene symbol in the search box to instantly visualize the expression data (AVP is displayed by default).
2. Optionally, click the button below the search box to switch the display of cells grouped in two forms (RNA cluster is displayed by default).

Prediction

The interface is designed to predict the blood cell types for single-cell RNA-seq datasets. Scmap is used to achieve cell type prediction and generate the visualization plot.

Usage:
1. Upload a tab-delimited format file containing the expression matrix. Each row should be a gene symbol and each column should be a single cell (UMI is recommended).
2. Click the Run button to start prediction. Cell Prediction (left panel) displays the single cells (highlighted in red color) in the ABC reference with minimum distances to the cells in the query. Original Atlas (right panel) displays the distributions of RNA clusters in the ABC reference. The table below summarizes the predicted cell type and prediction score for each single cell.
3. The size of file is less than 50M, which is about 1000 cells.

Mouse

The button is linked to our HSC transplantation work. We used single-cell RNA-seq to construct a comprehensive transcriptome reference in mouse homeostasis and guide the tracing of HSC transplantation dynamics in early one week window. Nature Cell Biology. 2020.

R package

abcCellmap is an R package to predict the cell types in the hematopoietic atlas for large data, which extends our ABC website function of cell prediction. Users can predict the cell types of hematopoietic cells by implementing two approaches (Scmap and Seurat).

Citation: Xiaowei Xie, Mengyao Liu, Yawen Zhang, Bingrui Wang, Caiying Zhu, Chenchen Wang, Qing Li, Yingying Huo, Jiaojiao Guo, Changlu Xu, Linping Hu, Aiming Pang, Shihui Ma, Lina Wang, Wenbin Cao, Shulian Chen, Qiuling Li, Sudong Zhang, Xueying Zhao, Wen Zhou, Hongbo Luo, Guoguang Zheng, Erlie Jiang, Sizhou Feng, Lixiang Chen, Xiuli An, Lihong Shi, Hui Cheng, Sha Hao, Ping Zhu, Tao Cheng, Single-cell Transcriptomic Landscape of Human Blood Cells, National Science Review, , nwaa180, https://doi.org/10.1093/nsr/nwaa180

This work is supported by Atlas of Blood Cells (ABC)