Journal: Nature neuroscience

Article Title: Gene expression correlates of the oscillatory signatures supporting human episodic memory encoding

doi: 10.1038/s41593-021-00803-x

Figure Lengend Snippet: a, Visualization of the 14 classes of cell-types identified from BA38 snATAC-seq data. Nuclei are displayed based on UMAP. Each dot represents a nucleus. Cell classes were annotated using the BA38 snRNA-seq data generated in this study. Excitatory neurons are highlighted in a gradient of blue colors, the inhibitory neurons in a gradient of red colors, and the non-neuronal cells in a gradient of turquoise colors. b , Transcription factor (TF) binding site enrichment for the three modules associated with cell-types (WM4, WM12, and WM21). Only WM12 tends to have enrichment of TF binding motifs (dots to the right of the dashed line). SMAD3 is shown as a top TF whose motif is enriched in WM12 module. Y-axis represents the −log 2 (FC) of the motif enrichment reported by FindMotifs in Seurat. X-axis represents the −log 10 (FDR) of the motif enrichment reported by FindMotifs in Seurat. Dashed line corresponds to FDR = 0.05 . c , Genome visualization tracks of snATAC-seq open chromatin regions representing SMAD3 binding sites in the promoter of the WM12 hub gene SHANK2 . The red ridge plot represents the snATAC-seq data. The SMAD3 binding sites are indicated in blue. d, Violin plot representing the log normalized expression (log(Norm Exp)) level (Y-axis) of SMAD3 for each cell-type defined by snRNA-seq. Adjacent dot plot represents the average expression (gradient) and percentage of cells (size) expressing SMAD3 . e,f, Immunohistochemistry of independent human temporal lobe specimens demonstrates the specific expression of SMAD3 in excitatory (CAMKII-α + ; e ) but not in inhibitory (GAD67 + ; e ) neurons, oligodendrocytes (OLIG2 + ; f ), nor astrocytes (GFAP + ; f ) in BA38.

Article Snippet: SMAD3 antibody was validated by R&D Systems using flow cytometry in human PC-3 cells and IHC in human pancreatic cancer tissue and human MDA-MB-231 cells .

Techniques: Generated, Binding Assay, Expressing, Immunohistochemistry

Journal: Cell reports

Article Title: DUX4 expression in cancer induces a metastable early embryonic totipotent program

doi: 10.1016/j.celrep.2023.113114

Figure Lengend Snippet:

Article Snippet: Fluorescein (FITC) AffiniPure Donkey Anti-Rat IgG , Jackson ImmunoResearch , Cat#712-095-150, RRID:AB_2340651.

Techniques: Recombinant, Electron Microscopy, Transfection, Bicinchoninic Acid Protein Assay, Amplification, SYBR Green Assay, Plasmid Preparation, DNA Purification, Control, Sequencing, Clone Assay, Software, Microscopy

Journal: Cell reports

Article Title: DUX4 expression in cancer induces a metastable early embryonic totipotent program

doi: 10.1016/j.celrep.2023.113114

Figure Lengend Snippet:

Article Snippet: Fluorescein (FITC) AffiniPure Donkey Anti-Mouse IgG , Jackson ImmunoResearch , Cat#715-095-151, RRID:AB_2335588.

Techniques: Recombinant, Electron Microscopy, Transfection, Bicinchoninic Acid Protein Assay, Amplification, SYBR Green Assay, Plasmid Preparation, DNA Purification, Control, Sequencing, Clone Assay, Software, Microscopy

Journal: Nature Communications

Article Title: GWAS for Interleukin-1β levels in gingival crevicular fluid identifies IL37 variants in periodontal inflammation

doi: 10.1038/s41467-018-05940-9

Figure Lengend Snippet: Expression and localization of IL-37 in human gingival tissue. a The sketch of five IL-37 isoforms. b PCR products amplified with specific primer pairs to different isoforms of IL-37 cDNA. c The relative mRNA levels of different isoforms of IL-37 in human gingival tissues from sites with periodontitis were quantitated using real time PCR with isoform-specific primers. d The relative mRNA levels of IL-37b (isoform1) in gingival tissues between health and periodontitis ( n ≥ 5/group). Data show the mean ± SD. *** p < 0.0001 (unpaired two-tailed Student’s t -test). e The representative level of IL-37 positive staining in epithelial and connective tissue of human gingival tissue from healthy and periodontitis patient using IHC. Scale bar is 200 µm. f The localization of IL-37b and CD138 were determined in serial slides of gingival tissue from periodontitis patient. The localization of IL-37 in human gingival tissue was mainly associated with epithelial and infiltrated plasma cells. The black circles with red number indicate representative region of IL-37 positive staining. A , B represent the low magnification of IL-37 and CD138 staining in human gingival tissue with Scale bar 200 µm. C – F represent the high magnification of two immune cells infiltrated regions in the connective tissue with Scale bar 20 µm. g , h represent the high magnification of epithelial cells layer with Scale bar 20 µm. g IL-37b and CD138 were co-localized in human gingival tissue of periodontitis patient by immunofluorescence using confocal microscope. The results represent CD138 (green), IL-37 (red), DAPI (blue), and bright field (white). The scale bar is 20 µm. Data shown here are representative of three independent experiments

Article Snippet: The slides were stained with anti-IL-37 antibody with 1:1000 dilution (rabbit anti-human, ThermoFisher SCIENTIFIC, PA5-30527), anti-CD138 with 1:150 dilution (goat anti-human CD138, R&D SYSTEMS, AF2780) antibody.

Techniques: Expressing, Amplification, Real-time Polymerase Chain Reaction, Two Tailed Test, Staining, Clinical Proteomics, Immunofluorescence, Microscopy