Fig. 2: Cell population dynamics.
From: Robust temporal map of human in vitro myelopoiesis using single-cell genomics
a Diagram illustrating the dynamic emergence of the different cell types over the course of the in vitro differentiation protocol (Discovery data set), weaker links are shown by discontinuous lines. b Schematic representation of the computational workflow used to compare transcription factor (TF) dynamics in vivo and in vitro. Briefly, TF activities were computed at branching points along the in vitro differentiation trajectory (Discovery data set) and were compared to TF activities in matched cell types in the in vivo human yolk sac6, gastrulation23 and foetal liver22 data sets. c RNA velocity analysis and PAGA graph abstraction of the cells present at day3 (Embryoid body (EB) formation) of the differentiation protocol (Discovery data set) showing the developmental relationships between cell types. d Transcription factor activities computed with DoRothEA for the identified cell types present at day3 of the in vitro differentiation protocol and matched cell types in the in vivo gastrulation data set23, relevant TFs are shown in bold, asterisks highlight significantly different activity vs its progenitor, Bonferroni adjusted p < 0.05. e RNA velocity analysis and PAGA graph abstraction of the cells present at day21 (EB myeloid differentiation) of the differentiation protocol (Discovery data set) showing the developmental relationships between the cell types. f Transcription factor activities computed with DoRothEA for the identified cell types present at day21 of the in vitro differentiation protocol and matched cell types in the in vivo yolk sac data set6, relevant TF shown in bold, asterisks highlight significantly different activity vs its progenitor, Bonferroni adjusted p < 0.05. g Same analysis as f with matched cell types in the in vivo foetal liver, skin and kidney data set22. h Violin plots showing the number of accessible peaks per cell type in the scATACseq Validation data set. Each plot shows a distinct lineage, asterisks highlight two-tailed t test Bonferroni adjusted p < 0.05. iPSC induced pluripotent stem cells, ATAC assay for transposase-accessible chromatin. Source data are provided in the Source data file.
