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Journal: Cell reports
Article Title: Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination
doi: 10.1016/j.celrep.2023.113454
Figure Lengend Snippet: KEY RESOURCES TABLE
Article Snippet:
Techniques: Virus, Recombinant, Staining, Cloning, Reporter Assay, Cell Culture, Software, Fluorescence, Imaging
Journal: Cancers
Article Title: Chemotherapeutics Used for High-Risk Neuroblastoma Therapy Improve the Efficacy of Anti-GD2 Antibody Dinutuximab Beta in Preclinical Spheroid Models
doi: 10.3390/cancers15030904
Figure Lengend Snippet: Impact of chemotherapy on percentage of ( A ) cytotoxic NK cells of lymphocytes and NK-cell-specific activating receptors. ( B – E ) 5 × 10 6 PBMCs were treated for 24 h under cell culture conditions with either carboplatin (2 µg/mL, open circles), cisplatin (1 µg/mL, open triangles), etoposide (0.5 µg/mL, open squares), vincristine (0.05 µg/mL, open diamonds), or the cyclophosphamide metabolite (4-HPC, 1 µg/mL, open hexagons). After 72 h of culturing, cells were analyzed for NKp30, NKp44, NKp46, NKG2D, and CD226 expression, using flow cytometry. ( A ) Relative number of cytotoxic NK cells (CD3 − , CD56 dim ) in lymphocytes. ( B – E ) Geometric mean fluorescence intensity (gMFI) of respective activating receptor of cytotoxic NK cells after chemotherapy. Data represent at least four biological replicates. Means and SEM are indicated as black lines and error bars, respectively. For statistical analysis, repeated measures ANOVA with appropriate post hoc test was used; * p < 0.05 vs., ** p < 0.01 versus untreated control (medium).
Article Snippet: Incubation with the following antibodies in a total volume of 100 μL was conducted for 20 min at RT: CD3-VioGreen (REA613, 1:200), CD56-APC-Vio770 (REA196, 1:200), CD226-VioBlue (REA1040, 1:50); CD335 (NKp46)-Vio Bright B515 (REA808, 1:50), CD337 (NKp30)-PE (REA823, 1:75),
Techniques: Cell Culture, Expressing, Flow Cytometry, Fluorescence, Control
Journal: Journal of Virology
Article Title: Simian-Human Immunodeficiency Virus SHIV.CH505 Infection of Rhesus Macaques Results in Persistent Viral Replication and Induces Intestinal Immunopathology
doi: 10.1128/JVI.00372-19
Figure Lengend Snippet: Representative flow plots demonstrating gating strategy used to identify B cells and innate immune subsets. Multicolor flow cytometry was used to identify B cells and innate immune subsets in whole blood, lymph node, rectum, and colon cells. (A) Depicted here are representative plots of stained lymph node cells from an uninfected rhesus macaque. Cells were identified by first excluding doublets using forward scatter (FSC) area and height properties, gating on CD45+ cells, excluding dead cells using an Aqua Live/Dead viability dye, and removing any remaining debris using FSC and side scatter (SSC) properties. Next, CD3− cells were identified, and B cells were gated as CD20+ HLA-DR+ cells. IgA- and IgG-expressing B cells were identified within CD20+ HLA-DR+ B cells. (B) Innate immune subsets, including neutrophils, monocytes, NK cells, ILC3s, mDCs, and pDCs, were identified in colon or whole blood. Depicted here are representative plots of stained whole blood cells from an uninfected rhesus macaque. As with B cells, cells were identified by excluding doublets using FSC area and height, gating on CD45+ cells, excluding dead cells, and removing debris with FSC/SSC properties. Next, CD3− cells were identified, and neutrophils were gated as CD11b+ CD14+ HLA-DR− SSChi cells. Monocytes were identified as CD11b+ CD14+ HLA-DR+ cells and then further classified as classical monocytes (CD14+ CD16−), intermediate monocytes (CD14+ CD16+), and nonclassical monocytes (CD14+ CD16+). After excluding CD11b+ CD14+ cells, B cells were excluded by gating out HLA-DR+ CD20+ cells, and then NK cells were identified as NKG2a/c+ CD8+. After excluding NK cells, ILC3s were identified as NKp44+ CD8−. After excluding ILC3s, antigen-presenting cells were identified as HLA-DR+ and further classified as mDCs (CD11c+) and pDCs (CD123+).
Article Snippet: Cells were further surface stained with predetermined optimal concentrations of the following antibodies with clones listed in parentheses, all from BD Biosciences unless otherwise stated: CD45-PE (phycoerythrin)-CF594 or -BV786 (D058-1283); CD3-AF700, -PerCP (peridinin chlorophyll protein), or -BV650 (SP34-2); CD4-BV605 (OKT4; BioLegend, San Diego, CA); CD8-BV650 (SK1) or -BV786 (RPA-T8); CD20-BV570 (2H7; BioLegend); HLA-DR-BV711 (L243; BioLegend); CD14-BV785 (M5E2; BioLegend); CCR6-BB515 or -BV650 (11A9); CCR5-PE (3A9); CD11c-PerCP-eFluor710 (3.9; eBioscience/Thermo Fisher Scientific, Waltham, MA); CD123-eFluor450 (6H6; eBioscience);
Techniques: Flow Cytometry, Staining, Expressing
Journal: Journal of Virology
Article Title: Simian-Human Immunodeficiency Virus SHIV.CH505 Infection of Rhesus Macaques Results in Persistent Viral Replication and Induces Intestinal Immunopathology
doi: 10.1128/JVI.00372-19
Figure Lengend Snippet: Minimal alteration of innate immune subsets during acute SHIV.CH505 infection. Neutrophil, NK, ILC3, mDC, pDC, and monocyte subsets were characterized in rectum and whole blood of SHIV.CH505-infected rhesus macaques by flow cytometry. (A to C) Percentage of neutrophils (A) (CD11b+ CD14+ HLA-DR− SSChi), NK cells (B) (NKG2a/c+ CD8+), and ILC3s (C) (NKp44+ CD8−) of CD45+ cells in rectum and whole blood at all time points. (D and E) Percentage of mDCs (D) (CD11c+) and pDCs (E) (CD123+) of HLA-DR+ antigen-presenting cells in rectum and whole blood at all time points. (F to H) Percentage of classical monocytes (F) (CD14+ CD16−), intermediate monocytes (G) (CD14+ CD16+), and nonclassical monocytes (H) (CD14+ CD16+) of total monocytes in rectum and whole blood at all time points. (I) Plasma levels of zonulin-1 were quantified by ELISA. In all panels, each animal is represented by a different symbol. Statistical significance between post-SHIV infection time points and pre-SHIV infection baseline was calculated using Friedman’s test and Dunn’s multiple-comparison test.
Article Snippet: Cells were further surface stained with predetermined optimal concentrations of the following antibodies with clones listed in parentheses, all from BD Biosciences unless otherwise stated: CD45-PE (phycoerythrin)-CF594 or -BV786 (D058-1283); CD3-AF700, -PerCP (peridinin chlorophyll protein), or -BV650 (SP34-2); CD4-BV605 (OKT4; BioLegend, San Diego, CA); CD8-BV650 (SK1) or -BV786 (RPA-T8); CD20-BV570 (2H7; BioLegend); HLA-DR-BV711 (L243; BioLegend); CD14-BV785 (M5E2; BioLegend); CCR6-BB515 or -BV650 (11A9); CCR5-PE (3A9); CD11c-PerCP-eFluor710 (3.9; eBioscience/Thermo Fisher Scientific, Waltham, MA); CD123-eFluor450 (6H6; eBioscience);
Techniques: Infection, Flow Cytometry, Clinical Proteomics, Enzyme-linked Immunosorbent Assay, Comparison