Physique S8

Physique S8. from our bulk RNA-Seq data.Physique S6. More details about MR TFs between bulk cDC1 and cDC2 that potentially drive the pre-commitment of pre-DCs. (A-B) Heatmap of MR TFs in bulk data (A) and single cell data (B). (C) t-SNE plot of all the single cells with global transcriptome, biological variable genes in pre-cDCs, DE genes between bulk cDC1 and cDC2 and the MR TFs, with pre-committed pre-cDC subsets marked. (D) Violin plot of the expression for the housing keep gene GABARAP. Physique S7. Trajectory analysis with Monocle2. Physique S8. Test our hypothesis on three published data sets. Test our hypothesis around the dataset of Breton et al., [5](A), Rabbit Polyclonal to CK-1alpha (phospho-Tyr294) Villani et al., [7](B) and the dataset in Fig. ?Fig.33 of See et al., 6(C). (PPTX 5054 kb) 12860_2019_199_MOESM1_ESM.pptx (4.9M) GUID:?9B29C50A-F4AA-4990-98AB-5521CA0504FA Additional file 2: Table VPC 23019 S1. The list of 380 genes that are differentially expressed between at least one pair of cell populations in imply expression and the gene clustering result. Table S2. A) The list of biological variable genes in pre-cDC of batch 2, B) enriched pathways of the variable genes and C) upstream regulators of the variable genes. VPC 23019 Table S3. The list of random selected genes to generate MDS plot in Fig. ?Fig.3d.3d. Table S4. The list of cell cycle genes from reactome to generate MDS plot in Fig. ?Fig.3e.3e. Table S5. Summary of grasp regulator transcriptional factors. Their expression level comparison was shown in groups bulk cDC2 VS. cDC1, single cell cDC2 VS. cDC1 and single cell pre-DC2 VS. pre-DC1. For the TFs that have targets enriched in the differentially expressed genes between cDC1 and cDC2, the evidence from ChEA database (version 2016) was followed. Table S6. The list of differentially expressed genes between two pre-cDC subpopulations. (ZIP 288 kb) 12860_2019_199_MOESM2_ESM.zip (289K) GUID:?485FE6BB-584D-490C-B561-6CD240CD3BA9 Data Availability StatementThe accession number for the RNA-Seq data reported in this paper is GEO: “type”:”entrez-geo”,”attrs”:”text”:”GSE89322″,”term_id”:”89322″GSE89322. Abstract Background Vintage dendritic cells (cDCs) play a central role in the immune VPC 23019 system by processing and presenting antigens to activate T cells, and consist of two major subsets: CD141+ cDC (cDC1) and CD1c+ cDC (cDC2). A populace of migratory precursor cells, the pre-cDCs, is the immediate precursors to both cDC subsets. Previous studies showed that there were two pre-committed pre-cDC subpopulations. However, the key molecular drivers of pre-commitment in human pre-cDCs were not investigated. Results To identify the key molecular drivers for pre-commitment in human pre-cDCs, we performed single cell RNA sequencing (RNA-Seq) of two cDC subsets and pre-cDCs, and bulk RNA-Seq of pre-cDCs and cDCs from human peripheral blood. We found that pre-DC subpopulations cannot be separated by either variable genes within pre-cDCs or differentially expressed genes between cDC1 and cDC2. In contrast, they were separated by 16 transcription factors that are themselves differentially expressed or have regulated targets enriched in the differentially expressed genes between bulk cDC1 and cDC2, with one subpopulation close to cDC1 and the other close to cDC2. More importantly, these two pre-cDC sub-populations are correlated with ratio of to expression level more than their individual expression level. We also verified these findings using three recently published datasets. Conclusions In this study, we demonstrate that single cell transcriptome profiling can reveal pre-cDCs differentiation map, and our results suggest the concept that combinatorial dose of transcription factors determines cell differentiation fate. Electronic supplementary material The online version of this article (10.1186/s12860-019-0199-y) contains supplementary material, which is available to authorized users. [10], [11], [10, 12], [13]. cDC2 dependent transcriptional factors include [14, 15], [16], [17]. There are some transcription factors implicated in both cDC1 and cDC2 development, such as Ets-family transcriptional factor ((([18]. However, the quality recipes of essential transcription factors for cDC1 and cDC2 subset commitment in human pre-cDCs have not been investigated. Our recent studies indicate that this lineage program is established early in hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) and transmitted to progeny and strengthened during cell division, and suggest that the lineage program is usually correlated with and orchestrated by combinatorial dose of multiple transcription factors [19]. How to identify such lineage program recipes as a commonality shared between distinct development stages has not yet been established. Here we statement a single cell transcriptomics study of pre-cDCs to investigate core transcriptional program underlying cDC1 and cDC2 lineages..