In this Perspective, Börner et al. discuss initiatives by 16 consortia to construct a Human Reference Atlas (HRA) comprising reference organs linked to tables that name major anatomical structures, cell types, plus biomarkers (ASCT+B) and present examples of HRA usage.

In this Perspective, Teichmann and colleagues present ongoing efforts from consortia of the Human Cell Atlas to harmonize and integrate data sources into a reference cell ontology and the contributions of cell ontologies to discovery.

Consistent integration and annotation of the vast data collected with advanced sequencing technologies will be key to unlocking cell biological insights. We now present a Focus of Perspective articles that discuss ways to improve knowledge consolidation towards generating a human reference atlas.

Wesley et al. describe the developmental trajectories of human foetal liver cell types at single-cell resolution and generate bipotential hepatoblast organoids, which can serve as a new platform to investigate human liver development.

Using single-cell analysis, Tan et al. map the cellular and spatial hierarchy and heterogeneity of eutopic endometrium and characterize ectopic peritoneal and ovarian endometriosis lesions from individuals receiving hormone treatment.

Rothová et al. deconstruct endodermal cell fate trajectories through single-cell transcriptomics and identify the central intermediate population transdifferentiating from an extra-embryonic to an embryonic identity.

Abe et al. profile, characterize and compare non-haematopoietic cells in normal human lymph nodes versus nodal lymphomas from patients, providing insights into stromal modelling in health and disease.

Zhang et al. perform single-cell RNA and B-cell receptor sequencing to characterize the transcriptomic profiles of B-cell acute lymphoblastic leukaemia cells at diagnosis, residual and relapse stages, uncovering the hypoxia pathway as a potential target for residual leukaemia cells.

Wang et al. analysed post-mortem samples of the lungs of patients with COVID-19 by bulk and single-nucleus RNA sequencing along with proteomics and discovered lung senescence as a feature of COVID-19 pathology.

Constructing a single-cell transcriptional map of primary human epidermal melanocytes, Belote et al. uncover distinct subpopulations of melanocytes, characterize dedifferentiation patterns associated with melanoma prognosis and uncover the unique cellular origens of acral melanoma.

Scheibner et al. demonstrate that, during gastrulation in the mouse, epithelial epiblast progenitors upregulate Foxa2 and form the definitive endoderm independently of a full EMT–MET cycle.

You et al. report single-cell ATAC-seq profiles of periphery immune cells from patients recovered from COVID-19, which reveals a global remodelling of the chromatin accessibility that may contribute to immune memory formation.

Saichi et al. performed single-cell RNA-seq analysis of antigen-presenting cells (APCs) isolated from the peripheral blood of patients with moderate and severe COVID-19 and uncovered defects in antiviral immune response in specific APC subsets.

Ponsioen et al. use a FRET‐based ERK biosensor EKAREN5 in patient‐derived organoids to show that EGFR activity amplifies signal transduction efficiency in KRAS or BRAF mutant MAPK pathways.

Lin et al. examine the process of clonal tuning during Flt3L-mediated emergency haematopoiesis, which leads to selective expansion of haematopoietic stem and progenitor cells that are primed to produce type 1 conventional dendritic cells instead of modulating cell fate.

Chen et al. perform single-cell analysis and identify transcriptomic remodelling in epithelial cells, macrophages, T cells, fibroblasts and endothelial cells, which together regulate prostate cancer progression.

Dong, Hao, Zhang, Zhu, Cheng et al. use single-cell RNA sequencing to characterize 28 haematopoietic cell populations and subsequently follow the fate and kinetics of HSCs upon transplantation in the mouse.

Pijuan-Sala et al. present a comprehensive single-nucleus open chromatin map of early mouse embryogenesis and validate the role of ETS transcription factor FEV in endothelial identity in zebrafish.

Yue, Zong, Li, Li, Zhang, Wu et al. introduce an in toto live-imaging system to track cardiac ventricle chamber formation at single-cell resolution for up to 1.5 days and digitally reconstruct cell dynamics.

Wang, Yu, Zhou, Song et al. profile cardiomyocytes and neighbouring cells from healthy adults and patients with heart failure and in recovery, and delineate their cellular compositions and interaction networks.

Baccin, Al-Sabah, Velten et al. use single-cell and spatially resolved transcriptomics to map the cellular, molecular and spatial organization of the endosteal, sinusoidal and arteriolar bone marrow niches.

Wang et al. map early cardiopharyngeal development in the chordate model Ciona and show that FGF–MAPK signalling maintains multipotency and promotes pharyngeal muscle fate, whereas Tbx1/10-Dach specify second heart lineage identity.

Using a multi-tier scRNA-seq and CRISP-seq approach, Giladi et al. define a transcriptional signature for the naive haematopoietic stem cell state, and follow progenitor plasticity and fate commitment under the influence of cytokines and growth factors.

Using scCOOL-seq, Li et al. simultaneously characterize the DNA methylation and chromatin accessibility of the same cell during human preimplantation development.

Gao et al. provide a comprehensive single-cell transcriptomic resource of four organs from the human fetal gastrointestinal tract and adult large intestine.

Knapp et al. analyse the heterogeneous molecular profiles and functions of CD49f human cord blood haematopoietic stem cells and report that a subset with CD33 expression has improved regenerative activity.

Ibarra-Soria et al. study cellular diversity, transcriptional signatures, lineage specification and somitogenesis on a single-cell level in E8.25 mouse embryos, and reveal the regulation of blood progenitor formation by the leukotriene pathway.

Velten et al. use single-cell transcriptomics and functional data to map the early lineage commitment of human haematopoietic stem cells as a continuous process of cells passing through transitory states rather than demarcating discrete progenitors.

With advanced high-throughput technologies, scientists can now use transcriptional signatures to study melanocytes as they become cancer. A new study identifies transcriptional programs at single-cell resolution across platforms and species, which enables prediction of melanoma prognosis and response to immune-checkpoint inhibitor therapy.

COVID-19 has led to a global pandemic, but the long-term immunological effects of the infection are only partially understood. A new study now provides important new clues by describing the transcriptional and epigenetic processes behind the immune memory of both adaptive and innate immune cells in individuals who have recovered from COVID-19.

Monocytes, plasmacytoid and conventional dendritic cells are crucial for antiviral immune responses. A new study now compares severe and moderate cases of COVID-19 and links defects in viral sensing, interferon and antigen presentation pathways, associated with upregulated apoptosis and inflammatory pathways, to high COVID-19 severity.

Prostate cancer is difficult to treat because of molecular, cellular and clinical heterogeneity. Using single-cell RNA sequencing, a recent study reveals unexpected transcriptomic reprograming in immune cells and non-immune components of the tumour microenvironment, which may lead to viable therapeutic approaches against prostate cancer.

Different types of stromal cells in the bone marrow associate to form niches that support differentiating blood cells and ensure lifelong production of all major blood lineages. A study now combines single-cell and spatial transcriptomics with imaging to infer the cellular composition and spatial architecture of specific niches.

The transition from a fertilized egg to a pluripotent and transcriptionally independent embryo requires multi-layered chromatin regulation. A study now provides simultaneous profiling of chromatin accessibility and DNA methylation in human preimplantation embryos at single-cell resolution.

Determining the differentiation potential of stem and progenitor cells is essential for understanding their function, yet our ability to do so is limited by the restrictions of experimental assays. Based on single-cell functional and molecular profiling experiments, a new computational approach shows how lineage commitment may occur in human haematopoiesis.