Extended Data Fig 5: Lymphoid lineages in fetal liver and NLT. | Nature

Extended Data Fig 5: Lymphoid lineages in fetal liver and NLT.

From: Decoding human fetal liver haematopoiesis

Extended Data Fig 5

a, PAGA analysis of fetal liver HSC/MPP and lymphoid cell types from Fig. 1b showing changes over four developmental stages. Lines symbolize connection; line thickness corresponds to the level of connectivity (low (thin) to high (thick) PAGA connectivity). b, c, Feature plots (b) and violin plots (c) showing ln-normalized median expression of selected known NK, ILC and T cell genes over gestation for early lymphoid/T lymphocyte cluster; **P < 0.001, ***P < 0.005 and ****P < 0.0001. d, Dot plot showing median-scaled ln-normalized median expression of V(D)J transcripts in fetal liver lymphoid cell types. Gene expression indicated by spot size and colour intensity. e, Heat map showing normalized expression of statistically significant, dynamically variable genes from pseudotime analysis for B cell lineage inferred trajectory (likelihood ratio test). Transcription factors are in bold. Morphology of liver pro-B and pre-B cells and B cells by Giemsa stain after cytospin. f, ln-normalized expression (mean ± s.e.m.) of TNFSF13B in Kupffer cells and NFKBIA in HSC/MPPs and cells in the B cell lineage across four developmental stages spanning 6–17 PCW; trend lines showing linear regression. g, PAGA connectivity scores of HSC/MPP and lymphoid cells from fetal liver, skin, kidney and yolk sac. h, ln-normalized median expression of selected known NK (top) and ILC precursor (bottom) marker genes and selected DEGs between liver (red), skin (blue) and kidney (green) visualized by violin plots (***P < 0.005 and ****P < 0.001). i, Violin plots showing ln-normalized median expression of selected known ILC and NK cell genes expressed in ILC precursors from fetal liver, skin and kidney.

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