2021
DOI: 10.1038/s41586-021-03852-1
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Abstract: The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct… Show more

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Cited by 272 publications
(210 citation statements)
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“…Approaches to single-cell profiling intestinal tissues vary between studies and depend on tissue availability and biological questions being asked. Current studies on intestinal immunity compare cells of healthy or IBD patients 15 18 , focus on regional differences 19 21 or investigate intestinal development 22 24 applying either in-depth or high-throughput methods, and increasingly combining other technologies such as V(D)J sequencing and spatial transcriptomics to better understand cell heterogeneity, lineage relationships and spatial locations in tissue 20 , 21 , 24 . Below we outline the current and emerging technologies and analysis tools for studying intestinal immunity.…”
Section: Scrnaseq Approaches To Studying Intestinal Immunitymentioning
confidence: 99%
“…Approaches to single-cell profiling intestinal tissues vary between studies and depend on tissue availability and biological questions being asked. Current studies on intestinal immunity compare cells of healthy or IBD patients 15 18 , focus on regional differences 19 21 or investigate intestinal development 22 24 applying either in-depth or high-throughput methods, and increasingly combining other technologies such as V(D)J sequencing and spatial transcriptomics to better understand cell heterogeneity, lineage relationships and spatial locations in tissue 20 , 21 , 24 . Below we outline the current and emerging technologies and analysis tools for studying intestinal immunity.…”
Section: Scrnaseq Approaches To Studying Intestinal Immunitymentioning
confidence: 99%
“…This is also becoming ever clearer in differentiated organism via the emerging cell map projects (e.g. [ 573 ]) As single-cell transcriptomics, proteomics, and metabolomics become possible, and individual cells are easily sorted in a fluorescence-activated cell sorter, one can contemplate studies in which the expression profiles even of large numbers of nominally isogenic cells are compared with their productivity simultaneously. This may even include understanding of the spatial distribution of proteins within individual cells [ 574 ].…”
Section: Looking To the Futurementioning
confidence: 99%
“…Skeletal muscle contains not only myogenic cells but also nonmyogenic cells such as endothelial cells, pericytes, smooth muscle cells, fibroblasts, and glial cells. However, none of clusters 6, 10, 11, 13, 14, and 15 appeared to be these nonmyogenic cells based on the expression levels of marker genes such as CDH5 and PECAM1 for endothelial cells (Elmentaite et al, 2021), NOTCH3 and MCAM for pericytes (Elmentaite et al, 2021), ACTA2 and MYH11 for smooth muscle cells (Kumar et al, 2017), COL1A and S100A4 for fibroblasts (Kumar et al, 2017), and FOXD3 and SOX10 for glial cells (Elmentaite et al, 2021) in these clusters (Supplementary File S2). It is possible that clusters 6, 10, 11, 13, 14, and 15 represented novel cell types in bovine skeletal muscle co-isolated with satellite cells or that they were inaccurately clustered by the computational program used.…”
Section: Cultured Bovine Satellite Cells Contain Subpopulations Whose Identities Remain To Be Determinedmentioning
confidence: 99%