Journal: Science (New York, N.Y.)

Article Title: A human cell atlas of fetal gene expression

doi: 10.1126/science.aba7721

Figure Lengend Snippet: (A) From each organ, we sampled 5,000 cells from each cell type (or all cells for cell types with fewer than 5,000 cells in a given organ). These were subjected to UMAP visualization on the basis of the top differentially expressed genes across cell types within each organ. Here they are colored by cell type labels, with colors as in Fig. 1C. In Fig. S10A, the same UMAP visualization is colored by tissue-of-origin. (B) Heatmap showing the relative expression of surface and secreted protein-coding genes, non-coding RNAs, and TFs (columns) in 77 main cell types (rows). UMI counts for genes are scaled for library size, log-transformed, and then mapped to Z scores and capped to [0, 3]. (C-D) Representative fluorescence microscopy of human fetal adrenal (C) or spleen (D) tissue, staining for for endothelium (CD34+), CSH1+, CSH2+ cells (ANXA1+; labeled by arrowhead) (C) or AFP+, ALB+ cells (AFP+ and labeled by arrowhead) (D). Nuclei are stained with blue DAPI. Bottom panels correspond to inset zooms. Scale bars, 50 μm (top) and 10 μm (bottom).

Article Snippet: The primary antibody we used: GYPA (R&D, MAB1228, 1:250), CD34 (R&D, AF7227, 1:250), CD34 (Novus, NBP2–32933, 1:250), ANXA1 (R&D, AF3770, 1:500), TNFRS10C (R&D, MAB6301, 1:500), AFP (Novus, NBP1–76275, 1:400), ALB (R&D, MAB1455, 1:10K), AHSG (R&D, AF1184, 1:400), and APOA1 (R&D, MAB36641, 1:250).

Techniques: Expressing, Transformation Assay, Fluorescence, Microscopy, Staining, Labeling

Journal: Science (New York, N.Y.)

Article Title: A human cell atlas of fetal gene expression

doi: 10.1126/science.aba7721

Figure Lengend Snippet: (A) Zoomed view of the erythropoiesis trajectory portion of Fig. 4B, colored by erythroid or megakaryocyte subtype. Black arrows show trajectory directionalities defined by (123). (B) Plots similar to (A), colored by the normalized expression of cell type-specific genes (FDR of 0.05 and over 2-fold expression difference between first and second ranked cell type), with the number of cell type-specific genes used and names of top few genes shown. UMI counts for these genes are scaled for library size, log-transformed, aggregated and then mapped to Z scores. (C) Point and box plot showing the proportion of blood cells that are EEPs for individual samples of different organs. Samples with low recovery of blood cells (<= 200) are excluded. (D) Representative fluorescence microscopy of human fetal adrenal tissue, staining for endothelium (CD34+) and erythroblasts (nucleated and GYPA+); nuclei stained with blue DAPI. The arrow indicates an GYPA+ erythroblast outside a CD34+ blood vessel. Scale bars, 10 μm. (E) Left: percentage of dissociated kidney and adrenal glands from newborn (P0) mice composed of enucleated erythrocytes and maturing erythroblasts. Right: distribution of maturing erythroblasts (proerythroblasts, ProE; basophilic erythroblasts, BasoE; polychromatophilic erythroblasts, PolyE; and orthochromatic erythroblasts, OrthoE) in the adrenal gland at P0 and in adult bone marrow. Error bars represent mean + SEM, n=3. (F) Representative images of maturing erythroblasts in the P0 adrenal gland and the adult bone marrow. Size bar = 10 μm. (G-H) UMAP visualization and marker-based annotation of macrophage subtypes colored by organ type (G) and subtype name (H). (I) Point and box plot showing the proportion of blood cells that are phagocytic macrophages for individual samples of different organs. Samples with low recovery of blood cells (<= 200) are excluded.

Article Snippet: The primary antibody we used: GYPA (R&D, MAB1228, 1:250), CD34 (R&D, AF7227, 1:250), CD34 (Novus, NBP2–32933, 1:250), ANXA1 (R&D, AF3770, 1:500), TNFRS10C (R&D, MAB6301, 1:500), AFP (Novus, NBP1–76275, 1:400), ALB (R&D, MAB1455, 1:10K), AHSG (R&D, AF1184, 1:400), and APOA1 (R&D, MAB36641, 1:250).

Techniques: Expressing, Transformation Assay, Fluorescence, Microscopy, Staining, Marker