Journal: The Journal of experimental medicine

Article Title: Landscape of mast cell populations across organs in mice and humans.

doi: 10.1084/jem.20230570

Figure Lengend Snippet: Figure 1. Mrgprb2+ and Mrgprb2neg MCs represent transcriptionally distinct MC populations. (A) UMAP plot of the scRNAseq performed on sorted peritoneal cavity. MCs. (B) UMAP plot of the scRNAseq performed on sorted immune cells from the back skin. Black arrowhead: MC population. (C). UMAP plot of the scRNAseq performed on sorted immune cells from the gut mucosa. Black arrowhead: MC population. (D) Violin plot of the expression of Mrgprb2, Mrgprb1, Mcpt4, Mcpt1, Kit, and Cpa3. (E) UMAP plot of all MC populations aggregated. (F) PCA showing the segregation between skin/peritoneal cavity and gut MCs. (G) Heatmap of 74 representative DEGs between MCs from gut, peritoneal cavity, and skin MC related. Characteristic genes and surface markers up- regulated in gut (green) or peritoneal cavity and skin MCs (red) are highlighted. (H and I) (H) Mrgprb2 and (I) Mcpt1 expression density on the aggregated populations. (J) Representative 3D confocal microscopy images of Avidin SRho (red), Mcpt1 (green), and DAPI (cyan) fluorescent signals of back skin, duo- denum, and colon. Arrows indicate gut mucosa and muscularis. Data are representative of three independent experiments. Bars = 100 (skin) and 70 (duodenum and colon) μm. DC, dendritic cell; NK, natural killer.

Article Snippet: Quality control numbers, ambient RNA decontamination, and analyses of scRNAseq samples Cell Ranger software (v.7.0.1; 10X Genomics) was used to demultiplex Illumina BCL files to FASTQ files (CellRanger mkfastq), to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting, and to produce gene–barcode matrices (CellRanger count).

Techniques: Expressing, Confocal Microscopy, Avidin-Biotin Assay

Journal: The Journal of experimental medicine

Article Title: Landscape of mast cell populations across organs in mice and humans.

doi: 10.1084/jem.20230570

Figure Lengend Snippet: Figure 3. MrgprB2+ and MrgprB2neg MCs have different hematopoietic origins and turnover kinetics. (A and B) Mrgprb2 (A) and Mcpt1 (B) expression density in MCs identified in the aggregated scRNAseq data of neonates (left) or adult (right) mice. (C) Representative 3D confocal microscopy images of Avidin

Article Snippet: Quality control numbers, ambient RNA decontamination, and analyses of scRNAseq samples Cell Ranger software (v.7.0.1; 10X Genomics) was used to demultiplex Illumina BCL files to FASTQ files (CellRanger mkfastq), to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting, and to produce gene–barcode matrices (CellRanger count).

Techniques: Expressing, Confocal Microscopy, Avidin-Biotin Assay

Journal: Nature

Article Title: Spatial multiomics map of trophoblast development in early pregnancy

doi: 10.1038/s41586-023-05869-0

Figure Lengend Snippet: a : Overview of the computational pipeline implemented for analysis of multimodal data. b - c : UMAP (uniform manifold approximation and projection) scatterplot of multimodal snATAC-seq data from donors P13, P14 and Hrv43 (n = 52,798 nuclei) coloured by cell state (b), donor, sample (10X library) or unbiased clustering labels (c). Data is annotated based on the corresponding single-nuclei RNA sequencing (snRNA-seq) cell state assignment. d : UMAP scatterplot of integrated multimodal single-nuclei ATAC sequencing (snATAC-seq) data for trophoblast only from donors P13, P14 and Hrv43 (n = 7449 nuclei) coloured by cell state, donor and sample (10X library). e : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell state. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). f : (Left) UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by sample. The manifold is calculated based on dimensionality reduction performed by MEFISTO (model with n = 9 factors). (Right) Scatterplot of UMAP coordinates obtained from the RNA expression data that were used as covariates for MEFISTO, coloured by cell state. g : Heatmap representing percentage of variance explained by each MEFISTO factor in each data modality. h : Smoothness along differentiation estimated with MEFISTO. i : UMAP scatterplot of multiome (snRNA-snATACseq) data of invading trophoblast cells from donor P13 (n = 1605 nuclei) coloured by cell cycle phase and MEFISTO factor values for important selected factors. j : Spearman’s rank correlation coefficients of each latent factor learned with MEFISTO and the number of genes per counts in snATAC-seq data (multiome). k : Gene set (RNA) enrichment analysis overview of MEFISTO factor 2 using two-sided parametric t-test, FDR is used to rank gene sets. l : Peak set (ATAC) enrichment analysis overview of MEFISTO factor 10 using two-sided parametric t-test, FDR is used to rank peak sets. Villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVTs (iEVTs), giant cells (GC), endovascular EVT (eEVT), dendritic cells (DC), lymphatic (l), maternal (m), fetal (f) Hofbauer cells (HOFB), innate lymphocytes (ILC), macrophages (M), monocytes (MO), natural killer (NK), perivascular (PV), decidual (d), epithelial (epi), stromal (S), fibroblasts (F), uterine smooth muscle cells (uSMC).

Article Snippet: For each sequenced snRNA-seq and ATAC–seq (multiome) library, we performed read alignment to custom made genome consisting of 10X Genomics’ GRCh38 3.0.0 pre-mRNA human reference genome and 10X Genomics Cell Ranger-Arc 1.0.1 ATAC genome, created following instructions from 10X Genomics: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references .

Techniques: RNA Sequencing, Sequencing, RNA Expression