Innate lymphoid cells (ILCs) are highly plastic immune cells that have been separated into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single-cell RNA sequencing and single-cell ATAC sequencing of ILCs isolated from the peripheral blood of healthy human donors, we show high transcriptional and epigenetic heterogeneity among circulating ILCs. We describe phenotypically distinct subclusters within main circulating ILC populations. We show diverse chromatin accessibility within main ILC subsets, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as a resource to infer ILC changes occurring in disease conditions. Overall, our work provides new insights in the complex human ILC biology. We anticipate our work to be a starting point to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients’ material.

This dataset was published by Falquet, Su, et al, iScience, 2023. The UMAPs and cell annotations presented in Figure 1 can be viewed in this Single Cell Portal study.

Available cell annotations are ILC_subset (i.e. main ILC1, cytotoxic ILC1, ILC2 and ILCP annotations) and ILC_subpopulation (ILC1, cytotoxic ILC1, ILC2a, ILC2b, ILCPa, ILCPb).

To view gene expression or chromatin accessibility data:

scRNAseq data, displayed in scRNAseq_UMAP: Search for gene symbol to view gene expression among ILCs.

scATACseq data, displayed in scATACseq_UMAP: Search for genome position to view accessibility of a single chromatin region, following positions on hg38. Separate the chromosome name and positions with “-”. For example, to view accessibility on chr1:100028671-100029237, search for “chr1-100028671-100029237”