HCA Data Explorer

A single cell immune cell atlas of human hematopoietic system

Human hematopoiesis is essential for producing blood cells and maintaining a healthy immune system. To provide a single-cell level characterization of the hematopoietic system, we profiled cells collected from cord blood, adult peripheral blood and adult bone marrow, to produce an immune cell atlas consisting of 1,453,784 single cells. Our atlas consists of a variety of single-cell RNA-seq assay types, such as standard assay, genetic pooling and cell hashing, which makes it an ideal dataset for benchmarking and developing new demultiplexing algorithms. We anticipate that our data will play an important role in addressing key questions of the human hematopoietic system, facilitating design of novel complete blood cell count tests and shedding light on new drug development as a health reference.

Orit Rozenblatt-RosenBroad Instituteorit@broadinstitute.org
Aviv RegevBroad Institutearegev@broadinstitute.org
Bo Li1
Monika S Kowalczyk1
Michal Slyper1
Gaublomme Jellert1
Marcin Tabaka1
Orr Ashenberg1
Julia Waldman1
Danielle Dionne1
Knecht Abigail1
Ma Hui1
Yiming Yang1
Orit Rozenblatt-Rosen1
Aviv Regev (Principal Investigator)1
1Broad Institute
Mallory Ann Freeberg
Danielle Welter
Enrique Sapena Ventura

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Analysis Portals


Project Label



Homo sapiens

Sample Type


Anatomical Entity

3 anatomical entities

Organ Part

2 organ parts

Selected Cell Types

5 cell types

Disease Status (Specimen)


Disease Status (Donor)


Development Stage

4 development stages

Library Construction Method

3 library construction methods

Nucleic Acid Source

single cell

Paired End


Analysis Protocol

adt_quantification, analysis, optimus_post_processing_v1.0.0, optimus_v4.2.2, quantification

File Format

6 file formats

Cell Count Estimate


Donor Count

bam127 file(s)csv5 file(s)fastq.gz1,548 file(s)h5258 file(s)h5ad8 file(s)loom129 file(s)