Journal: Nature Communications

Article Title: A single-cell transcriptional atlas reveals resident progenitor cell niche functions in TMJ disc development and injury

doi: 10.1038/s41467-023-36406-2

Figure Lengend Snippet: a UMAP plot of 9 clusters (refer to Methods for the codes used). The macrophage cluster (MPhs, Cluster 2) is marked in yellow. b Violin plot of C1qa/C1qb/C1qc in the 4 principal cell types. Expression values are nonnormalized. c Representative images of TMJ discs subjected to immunofluorescence staining for C1QA at different stages. Green: C1QA; blue: DAPI. A: anterior band, P: posterior band, white dotted lines: boundary of the discs. N = 6 independent animals with similar results. Scale bar: 50 μm. d Flow cytometry plot of MPhs stained with C1QA antibodies. The dot plots display representative data (left). The quantifications of %C1QA + cells (mean + /-SD) at different stages are presented (right). N = 3 independent biological samples. The one-way ANOVA with Tukey’s multiple comparison test was used for analysis, * p = 0.0413, ** (3d vs. 78-82w) p = 0.0012, ** (3w vs. 78-82w) p = 0.0044. Abbreviations: FSC-A: forward scatter area. e UMAP plot of 9 clusters (refer to Methods for the codes used). The endothelial cluster (ECs, Cluster 5) is marked in green. f Violin plot of Pecam1 in the 4 principal cell types. Expression values are nonnormalized. g Representative images of TMJ discs subjected to immunofluorescence staining for PECAM-1 at different stages. Green: PECAM-1; blue: DAPI. A: anterior band, P: posterior band, white dotted lines: boundary of the discs. N = 6 independent animals with similar results. Scale bar: 50 μm. h Flow cytometry plot of ECs stained with PECAM-1 antibodies. The dot plots display representative data (left). The quantifications of % PECAM-1 + cells (mean + /-SD) at different stages are presented (right). N = 3 independent biological samples. The one-way ANOVA with Tukey’s multiple comparison test was used for data analysis, * p = 0.0414, ** p = 0.0089. Abbreviations: FSC-A: forward scatter area.

Article Snippet: Primary antibodies, which included antibodies against CD90.2 (14-0902-82, Invitrogen, USA) diluted to 1:100 in blocking solution, PECAM-1 (550274, BD Pharmingen, USA) diluted to 1:100 in blocking solution, NOTCH3 (PA519515, Invitrogen, USA) diluted to 1:400 in blocking solution, and C1QA (NBP1-51139, Novus, USA) diluted to 1:200 in blocking solution, were incubated at 4 °C overnight.

Techniques: Expressing, Immunofluorescence, Staining, Flow Cytometry, Comparison

Journal: Diabetology & Metabolic Syndrome

Article Title: Single-cell RNA sequencing reveals roles of unique retinal microglia types in early diabetic retinopathy

doi: 10.1186/s13098-024-01282-3

Figure Lengend Snippet: Inflammatory and activation characteristics of microglial subtypes. A Three-dimensional UMAP plot of microglia and macrophages. The different colors correspond to different cell types. B Boxplot showing the marker genes of microglia and macrophages. According to their different gene expression profiles, the microglia were categorized into three groups: Egr2 + M1 microglia ( C1qa + , Ccr5 + , Egr2 + ), Egr2 − M1 microglia ( C1qa + , Ccr5 + , Egr2 − ) and M2 microglia ( C1qa + , Ccr5 − , Egr2 − ). Macrophages highly expressed Cxcr4 . C Immunofluorescence labeling for C1qa (red) and Ccr5 (green) and DAPI nuclear staining (blue) in the rat retina. M1 microglia are indicated by arrows, and M2 microglia are indicated by arrowheads (above, 63 ×). Immunofluorescence labeling for Ccr5 (red) and Egr2 (green) and DAPI nuclear staining (blue) in the rat retina. Egr2 + M1 microglia are indicated by arrows, and Egr2 − M1 microglia are indicated by arrowheads (below, 63 ×). Scale bar 20 µm. D Immunofluorescence labeling for C1qa (red) and Ccr5 (green) and DAPI nuclear staining (blue). M2 microglia are indicated by arrows (left, 20 ×). Immunofluorescence labeling for Ccr5 (red) and Egr2 (green) and DAPI nuclear staining (blue). Egr2 + M1 microglia are indicated by arrowheads, and Egr2 − M1 microglia are indicated by asterisks (right, 20 ×). Scale bar 50 µm. E Plot showing the pathways enriched in M2 microglia in GSEA. The threshold limits were a p value < 0.1 and a FDR q-value < 0.25. F Heatmap showing the average expression of inflammatory mediators in microglia and macrophages. The plot is ordered by the three gene categories (labels on left). High expression is in red, and low expression is in blue. G Bubble plots showing the expression of inflammatory cytokines in microglia subpopulations from different data sets. The size of each circle is proportional to the percentage of gene expression. High expression is shown in blue, and low expression is shown in gray. Mouse_2, Mouse_3 and Mouse_brain were obtained from normal mouse samples. H Bubble plot showing the expression of inflammatory mediators in Egr2 + M1 microglia and Egr2 − M1 microglia in different stages of DR. The size of each circle is proportional to the percentage of gene expression. High expression is shown in red/yellow, and low expression is shown in gray

Article Snippet: Antibodies used in this study were as follows: Purified mouse Complement Component C1qA Antibody (NOVUS NBP1-51,139); Rabbit Monoclonal EGR2 Antibody (JG78-39); Rat monoclonal [HEK/1/85a] to CCR5 (Abcam ab11464); Cy3–conjugated Affinipure Goat Anti-Mouse IgG(H + L) (SA00009-1); Goat Anti-Rabbit IgG(H + L), Mouse/Human ads-APC (SBA-4050-11S).

Techniques: Activation Assay, Marker, Gene Expression, Immunofluorescence, Labeling, Staining, Expressing

Journal: Diabetology & Metabolic Syndrome

Article Title: Single-cell RNA sequencing reveals roles of unique retinal microglia types in early diabetic retinopathy

doi: 10.1186/s13098-024-01282-3

Figure Lengend Snippet: Activation mechanism of microglia. A Volcano plot showing the DEGs between Egr2 + M1 microglia and Egr2 − M1 microglia. The adjusted P value and gene expression (log fold change) were used for the plot. B PPI network showing the highly expressed proteins of Egr2 + M1 microglia. The size and color represent the combined score of each protein. Significant proteins are marked with red circles. C Heatmap showing the enrichment of pathways in different subtypes of microglia in GSVA. High expression is in red, and low expression is in blue. D Violin plot showing the expression of inflammatory receptors in the three groups of microglia. E Gating strategy for sorting Egr2 + M1 cells. Egr2 + M1 cells are gated as Ccr5 + C1qa + Egr2 + cells. F The bar graph shows the qPCR results for Egr2 + M1 cells. * denotes a p-value of < 0.05, ** denotes a p-value of < 0.01 and *** denotes a p-value of < 0.001. The levels of inflammatory cytokines like Tnf and members of the AP-1 family were significantly elevated in Egr2 + M1 cells compared to normal cells

Article Snippet: Antibodies used in this study were as follows: Purified mouse Complement Component C1qA Antibody (NOVUS NBP1-51,139); Rabbit Monoclonal EGR2 Antibody (JG78-39); Rat monoclonal [HEK/1/85a] to CCR5 (Abcam ab11464); Cy3–conjugated Affinipure Goat Anti-Mouse IgG(H + L) (SA00009-1); Goat Anti-Rabbit IgG(H + L), Mouse/Human ads-APC (SBA-4050-11S).

Techniques: Activation Assay, Gene Expression, Expressing

Journal: PLoS ONE

Article Title: Ovariectomy and Subsequent Treatment with Estrogen Receptor Agonists Tune the Innate Immune System of the Hippocampus in Middle-Aged Female Rats

doi: 10.1371/journal.pone.0088540

Figure Lengend Snippet: Expression of complement and cytokine genes in the hippocampus of middle-aged female rats.

Article Snippet: C1qa , Rn01519903_m1 , 6.625.

Techniques: Expressing

Journal: Foods

Article Title: Transcriptional Biomarkers and Immunohistochemistry for Detection of Illicit Dexamethasone Administration in Veal Calves

doi: 10.3390/foods11121810

Figure Lengend Snippet: List of selected targets for Gene expression study, reference sequences, amplicon sizes and supplier references for each Taqman assay. Reference gene for data normalisation marked with *.

Article Snippet: Bt03218751_m1 , C1QA , NM_001014945.2 , 65 bp.

Techniques: Gene Expression, Amplification, TaqMan Assay