Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone marrow-derived hematopoietic progenitors that migrate through the bloodstream. The current understanding of the nature of thymic immigrants is largely based on data from pre-clinical models. Here, we employed single-cell RNA sequencing (scRNA-seq) to examine the immature postnatal thymocyte population in humans. Integration of bone marrow and peripheral blood precursor datasets identified two putative thymus seeding precursors that varied in expression of CD7; CD10; and the homing receptors CCR7, CCR9, and ITGB7. Whereas both precursors supported T cell development, only one contributed to intrathymic dendritic cell (DC) differentiation, predominantly of plasmacytoid dendritic cells. Trajectory inference delineated the transcriptional dynamics underlying early human T lineage development, enabling prediction of transcription factor (TF) modules that drive stage-specific steps of human T cell development. This comprehensive dataset defines the expression signature of immature human thymocytes and provides a resource for the further study of human thymopoiesis. Overall design: Single cell transcriptional libraries were generated from CD34+ human post-natal thymocyte samples using the 10X Genomics Chromium 3’ sequencing V2 kit.
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Atlas
Analysis Portals

Project Label
LavaertHumanThymusSpecies
Homo sapiens
Sample Type
specimens
Anatomical Entity
thymus
Organ Part
thymus
Selected Cell Types
thymocyte
Disease Status (Specimen)
Unspecified
Disease Status (Donor)
congenital heart disease
Development Stage
Library Construction Method
Nucleic Acid Source
single cell
Paired End
falseAnalysis Protocol
analysis _protocol1File Format
Cell Count Estimate
70.0kDonor Count
10