Journal: BMC Genomics

Article Title: Epidermal growth factor dampens pro-inflammatory gene expression induced by interferon-gamma in global transcriptome analysis of keratinocytes

doi: 10.1186/s12864-025-11237-1

Figure Lengend Snippet: EGF modifies the IFN-g-regulated transcriptome and globally attenuates IFN-g-induced gene expression in human keratinocytes. a Heatmap showing differentially expressed genes (FDR < 0.01) induced by IFN-g alone, EGF alone, or IFN-g plus EGF (excluding genes that were not differentially expressed in any treatment group relative to control). FDR distributions and volcano plots (with dashed line corresponding to FDR cut-off of 0.01) showing log2 fold change in gene expression, relative to control, in keratinocytes following treatment with ( b ) IFN-g alone, and ( c ) IFN-g plus EGF. d Venn-diagram showing differentially expressed genes (FDR < 0.01) induced by IFN-g and/or EGF. e Fold change of the top 10 genes induced after treatment with IFN-g alone; asterisks above CXCL10 and GBP5 correspond to statistically significant interaction FDR values (*FDR < 0.05; ** FDR < 0.01) and indicate that EGF modified (attenuated) the differential gene expression induced by IFN-g (detailed information in Supplementary Table 3)

Article Snippet: Human IFN-γ (Peprotech, NJ) and EGF (Promega, WI) were resuspended in DMEM (200 mg/mL and 2000 ng/ml respectively) and stored at −80 °C.

Techniques: Gene Expression, Control, Modification

Journal: BMC Genomics

Article Title: Epidermal growth factor dampens pro-inflammatory gene expression induced by interferon-gamma in global transcriptome analysis of keratinocytes

doi: 10.1186/s12864-025-11237-1

Figure Lengend Snippet: IFN-g-regulated genes and associated pathways most affected by EGF in keratinocytes. a Heatmap showing log2 fold change in gene expression of IFN-g-regulated genes whose expression was either significantly dampened or augmented by EGF ( N = 160, interaction FDR < 0.05). Note that not all genes fit on the axis to the right of the heatmap but are shown in Supplementary Table 3 with detailed data. b Gene network from Network Topology Analysis (NTA) of IFN-g-regulated genes whose expression was either 2-fold higher or lower when EGF was added; genes in the top enriched GO Biological Process category are shaded in red (‘Antigen processing and presentation of exogenous peptide antigen via MHC class II’ [GO:0019886]; FDR = 2.65 × 10 −7 ); blue shading of CXCL10 denoting it as the most strongly upregulated gene by IFN-g to be dampened by EGF treatment. c Volcano plot showing the enriched KEGG pathways within the list of IFN-g-induced genes to be significantly dampened or augmented (interaction FDR < 0.05) by EGF treatment. Dashed line represents statistical significance cutoff of FDR 0.05. d Enrichment plot of the most significantly enriched KEGG pathway (KEGG:04060): ‘Cytokine-cytokine receptor interaction’ (NES = 2.11, P < 0.0001, FDR = 0.003); CXCL10 had the highest ranked list metric (10.5) identifying it as the top gene driving this enrichment signal

Article Snippet: Human IFN-γ (Peprotech, NJ) and EGF (Promega, WI) were resuspended in DMEM (200 mg/mL and 2000 ng/ml respectively) and stored at −80 °C.

Techniques: Gene Expression, Expressing

Journal: Journal of visualized experiments : JoVE

Article Title: Dissection and isolation of murine glia from multiple central nervous system regions

doi: 10.3791/61345

Figure Lengend Snippet: Table of Materials

Article Snippet: Name of Material/ Equipment Company 0.05% Trypsin and 0.53 mM EDTA Gibco 12-Well Plates Greiner Bio-One 1X PBS pH 7.4 Gibco 32% Paraformaldehyde Electron Microscopy Sciences 50 mL, 25 cm 2 cell culture flask Greiner Bio-One Antibiotic-Antimycotic 100X Gibco B-27 Supplement 50X Gibco Bovine serum albumin Sigma Confocal Microscope Zeiss DAPI ThermoFisher DMEM (1X), high glucose with Na pyruvate Gibco Dnase I Sigma Fetal bovine serum heat inactivated Gibco Fibronectin from bovine plasma Sigma Fine stitch Scissors Sklar Goat anti-rabbit IgG Alexa Fluor 488 Invitrogen Goat anti-rat IgG Alexa Fluor 555 Invitrogen Hanks' Balanced Salt Solution (w/o Ca or Mg) ThermoFisher L-glutamine, 200mM Gibco Murine epidermal growth factor ThermoFisher Murine IFN-γ Peprotech Murine PDGF-AA Peprotech Neurobasal Gibco Normal goat serum Sigma Operating Scissors Surgi-OR Poly-D-Lysine 12 mm #1 German Glass Coverslip Corning Biocoatt Prolong Gold Antifade Reagent Cell Signaling Technology Rabbit anti-Iba1 Wako Rabbit anti-NG2 Chondroitin Proteoglycan Millipore Rat anti-GFAP ThermoFisher Rat anti-myelin basic protein Abcam Sharp Tip Scissors Surgi-OR Stereo Microscope Leica Tissue Forceps Sklar Triton X-100 Fisher Bioreagents Trypsin Inhibitor (from chicken egg white) Sigma Catalog Number Comments/Description 25300054 Tissue dissociation 665 180 Cell culture plate 10010031 Standard reagent 15714-S Fixative 690 175 Cell culture (T25) flask 15240-096 Media component 17504-044 Media component A9647-50G Antibody diluent LSM 800 Confocal for imaging D1306 Nuclear stain 11995040 Media component 10104159001 Tissue dissociation A3840001 Media component F1141-1MG Cell adherent 64-3260 Dissection tools A11008 Secondary staining antibody A21434 Secondary staining antibody 14170120 Tissue dissociation 20530081 Media component PMG8044 Media component 315-05-20UG Media component 315-17 Media component 21103-049 Media component G9023 Blocking solution component 95-272 Dissection tools 354086 Cell adherent 9071S Mounting Media 019-19741 Primary antibody ab5320 Primary antibody 13-0300 Primary antibody ab7349 Primary antibody 95-104 Dissection tools S4 E Stereo Zoom Microscope Microscope for dissection 66-7644 Dissection tools BP151-100 Cell permabilization 10109878001 Tissue dissociation Open in a separate window Table of Materials.

Techniques: Electron Microscopy, Cell Culture, Microscopy, Clinical Proteomics, Imaging, Staining, Dissection, Blocking Assay