Journal: Nature Communications

Article Title: IFN-β is a macrophage-derived effector cytokine facilitating the resolution of bacterial inflammation

doi: 10.1038/s41467-019-10903-9

Figure Lengend Snippet: Non-phagocytic resolution phase macrophages express IFN-β. a , b Male mice were injected intraperitoneally with zymosan A (1 mg/mouse) followed by an injection of PKH2-PCL at 62 h. After 4 h, the peritoneal cells were recovered and immuno-stained for F4/80 and CD11b. Then, F4/80 + macrophages were sorted based on the extent of PKH2-PCL acquisition (PKH2 + /− populations; >98% purity) using the FACSAria III sorter (illustrated in ( a ). The collected cells were immediately used for RNA extraction (with RNA integrity value above 7.5), and a gene expression microarray analysis was performed using Illumina hiSeq 2500. Differential gene expression analysis and gene ontology (GO) enrichment were performed for genes that were significantly upregulated ( b , left panel) or downregulated ( b , right panel) in non-phagocytic/satiated (PKH2-PCL lo ) macrophages in comparison to phagocytic (PKH2-PCL hi ) ones. The results indicate the statistical significance of the GO term and the percentage of enrichment is presented. c – e Expression of IFN-β and ISG15 in sorted satiated and phagocytic macrophages. Representative results ( c ) and mean ± SEM ( d , e ) for three independent experiments. * P < 0.05 (Student’s t test). g , h Peritoneal exudates were collected from unchallenged mice (0 h) or following peritonitis for 4–96 h. IFN-β content in cell-free fluids was determined by ELISA ( f ). Results are mean ± SEM from three (24, 72, 96 h) or four (0, 4, 48 h) mice. * P < 0.05, ** P < 0.01, *** P < 0.005 (Tukey’s HSD). Alternatively, resolution phase macrophages were recovered 66 h post peritonitis initiation (PPI) and incubated with TGF-β (5 ng/ml), poly (I:C) (4 μg/ml) or apoptotic cells (AC, at a ratio of 1:5) for 24 h. Culture supernatants were then collected and IFN-β content was measured ( g ). Culture media from apoptotic cells served as control. Results are representative from three independent experiments. * P < 0.05, ** P < 0.01, *** P < 0.005 (Tukey’s HSD). Source data are provided as a Source Data file

Article Snippet: Peritoneal exudates and bronchoalveolar lavage fluid were collected at the indicated times and the levels of IFN-β in cell-free fluids were determined by VeriKine-HS Mouse Interferon Beta Serum ELISA Kit (Pestka Biomedical Laboratories, Inc).

Techniques: Injection, Staining, RNA Extraction, Gene Expression, Microarray, Comparison, Expressing, Enzyme-linked Immunosorbent Assay, Incubation, Control

Journal: Nature Communications

Article Title: IFN-β is a macrophage-derived effector cytokine facilitating the resolution of bacterial inflammation

doi: 10.1038/s41467-019-10903-9

Figure Lengend Snippet: IFN-β favors macrophage reprogramming during the resolution of inflammation. a – d Macrophages were recovered from peritoneal exudates of male Ifnb +/+ or Ifnb − / − mice at 48–66 h PPI and cultured with LPS (1 μg/ml) for 24 h. Culture supernatants were then collected and levels of IL-10 ( a ), IL-6 ( b ), IL-12 ( c ) and CCL3 ( d ) were determined by selective ELISAs. Results are means ± SEM from four independent experiments. * P < 0.05, *** P < 0.005 (Tukey’s HSD). e – f Macrophages were recovered from peritoneal exudates of Ifnb +/+ mice at 48–66 h PPI and cultured with mouse IFN-β or IFN-α (20 ng/ml each) for 48 h. Then, culture supernatants were collected and levels of IL-10 ( e ) and IL-12 ( f ) were determined by ELISA. Results are means ± SEM (n = 4). *** P < 0.005 (Tukey’s HSD). g Macrophages were recovered from peritoneal exudates of Ifnb +/+ mice 48–66 h PPI and incubated with IFN-β (20 ng/ml) for 48 h. The cells were then immunostained for F4/80 and CD11b and the percentage of CD11b low macrophages was determined by flow cytometry. Results are means ± SEM from three independent experiments. *** P < 0.005 (Tukey’s HSD). h – i Mice undergoing peritonitis were treated with IFN-β (20 ng/mouse, i.p.) or vehicle at 24 h PPI. Peritoneal macrophages were collected at 48 h PPI, lysed and immunoblotted for 12/15-LO, arginase 1, ISG15 and GAPDH. Representative blots ( h ) and densitometry analysis (means ± SEM) ( i ) for three independent experiments. * P < 0.05 (Student’s t test). Source data are provided as a Source Data file

Article Snippet: Peritoneal exudates and bronchoalveolar lavage fluid were collected at the indicated times and the levels of IFN-β in cell-free fluids were determined by VeriKine-HS Mouse Interferon Beta Serum ELISA Kit (Pestka Biomedical Laboratories, Inc).

Techniques: Cell Culture, Enzyme-linked Immunosorbent Assay, Incubation, Flow Cytometry

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Microarray, Recombinant, Sample Purification, Isolation, Derivative Assay, shRNA, Construct, CRISPR, Plasmid Preparation, Software

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: A. Experimental schematic to profile BAF complex localization and other chromatin changes in hTERT-MSCs upon 24 hours adipogenesis. B. edgeR analysis of differential occupancy of BAF complexes (SMARCA4) on the genome upon 24 hours adipogenesis. C. HOMER motif analysis of sites that gain BAF complex (SMARCA4) occupancy upon 24 hours adipogenesis. D. Heatmap of SMARCA4, CEBPB, H3K27ac, and ATAC-seq peaks over sites that gain BAF complex (SMARCA4) occupancy upon 24 hours adipogenesis (“SMARCA4 targets”). E. Experimental schematic to define the specific role for BAF complexes in adipogenesis using small molecule-mediated inhibition of BAF complex ATPase activity with compound 12 (CMP12). F. Heatmap of SMARCA4, CEBPB, H3K27ac, and ATAC-seq peaks upon DMSO or CMP12 treatment in base or adipogenic media for 24 hours over SMARCA4 gained sites in the DMSO adipogenesis condition. G. Comparison of changes in RNA in the CMP12 and DMSO treatment conditions upon adipogenesis. Dark blue circles are genes that are not as up-regulated or are more down-regulated upon adipogenesis with CMP12 treatment compared to DMSO (CMP12-attenuated gene). Light blue circles are a subset of CMP12-attenuated genes that are also nearest to sites that gain BAF complexes (SMARCA4) upon adipogenesis in the DMSO condition (CMP12-attenuated gene and SMARCA4 target). H. Gene ontology analysis of CMP12-attenuated gene and SMARCA4 targets. I. Heatmap of logFC in expression of genes in DMSO and CMP12 conditions upon adipogenesis. J. Track examples at the CD36, ELOVL6 and WNT5A loci. See also Figure S4.

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Inhibition, Activity Assay, Comparison, Expressing

Journal: Molecular cell

Article Title: The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

doi: 10.1016/j.molcel.2022.03.019

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mesenchymal Stem Cell Growth Kit for Adipose and Umbilical-derived MSCs - Low Serum , ATCC , Cat# PCS-500-040.

Techniques: Microarray, Recombinant, Sample Purification, Isolation, Derivative Assay, shRNA, Construct, CRISPR, Plasmid Preparation, Software

Journal: Reproductive Biology and Endocrinology : RB&E

Article Title: A promising future for endometriosis diagnosis and therapy: extracellular vesicles - a systematic review

doi: 10.1186/s12958-022-01040-y

Figure Lengend Snippet: Key characteristics of studies of extracellular vesicles in endometriosis

Article Snippet: Shan 2021 [ ] , Human ( n = 5 for RNA seq, n = 80 for validation) , Human ( n = 6 for RNA seq, n = 80 for validation) , Serum , ExoRNeasy Serum/Plasma Midi Kit (#76,214, Qiagen) , Yes , lncRNAs (seq) Ten lncRNAs validated with RT-qPCR , Potential diagnostic marker RP3-399L15.2 AUC 0.86, Sn 67%, Sp 98%. Using combination of RP3-399L15.2 and CH507-513H4.6 AUC 0.90, Sn 80%, Sp 85%. , Not discussed, but potential therapeutic targets , Not discussed , Endometriomas only.

Techniques: Diagnostic Assay, Isolation, Derivative Assay, Migration, Biomarker Discovery, Activity Assay, Inhibition, Expressing, Over Expression, Clinical Proteomics, Control, RNA Sequencing, Marker, In Vivo, In Vitro, Microarray, Cell Culture

Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods from current investigations regarding miRNAs in periodontal disease.

Article Snippet: Zahran et al. 2015 [ ] , 20 healthy controls, 40 potentially malignant disorders, 20 OSCC, 20 recurrent aphthous stomatitis , Unstimulated saliva supernatant , miRNeasy serum/plasma extraction kit (Qiagen) , — , RT-qPCR SYBR green PCR kit (Qiagen) , SNORD68 , One-way ANOVA, F -test, Dunnett t -test, Scheffe's multiple comparison, two-tailed tests , miR-21, miR-184, miR-145.

Techniques: Comparison, RNA Extraction, Biomarker Discovery, Control, In Vitro, Microarray, Isolation, TaqMan microRNA Assay, SYBR Green Assay, Labeling, Real-time Polymerase Chain Reaction, Virus, Quantitative RT-PCR, In Vivo, Expressing, Mann-Whitney U-Test

Journal: BioMed Research International

Article Title: MicroRNAs as Salivary Markers for Periodontal Diseases: A New Diagnostic Approach?

doi: 10.1155/2016/1027525

Figure Lengend Snippet: Comparison of methods for salivary miRNA diagnosis.

Article Snippet: Zahran et al. 2015 [ ] , 20 healthy controls, 40 potentially malignant disorders, 20 OSCC, 20 recurrent aphthous stomatitis , Unstimulated saliva supernatant , miRNeasy serum/plasma extraction kit (Qiagen) , — , RT-qPCR SYBR green PCR kit (Qiagen) , SNORD68 , One-way ANOVA, F -test, Dunnett t -test, Scheffe's multiple comparison, two-tailed tests , miR-21, miR-184, miR-145.

Techniques: Comparison, Biomarker Discovery, Extraction, Control, Marker, Isolation, Mann-Whitney U-Test, TaqMan microRNA Assay, TLDA Assay, Expressing, Microarray, Lysis, SYBR Green Assay

Journal: Cancer cell

Article Title: Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma

doi: 10.1016/j.ccell.2017.07.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Biological Samples Primary tumour samples Multiple tissue source sites, processed through the Biospecimen Core Resource See Methods: Experimental Model and Subject Details Critical Commercial Assays Genome-Wide Human SNP Array 6.0 ThermoFisher Scientific Cat: 901153 Infinium HumanMethylation450 BeadChip Kit Illumina Cat: WG-314-1002 EZ-96 DNA Methylation Kit Zymo Research Cat: D5004 Illumina Barcoded Paired-End Library Preparation Kit Illumina https://www.illumina.com/techniques/sequencing/ngs-library-prep.html TruSeq RNA Library Prep Kit Illumina Cat: RS-122-2001 TruSeq PE Cluster Generation Kit Illumina Cat: PE-401-3001 Phusion High-Fidelity PCR Master Mix with HF Buffer New England Biolabs Cat: M0531L VECTASTAIN Elite ABC HRP Kit (Peroxidase, Standard) Vector Lab Catalog: PK-6100 Deposited Data Raw and processed clinical, array and sequence data.

Techniques: Genome Wide, DNA Methylation Assay, Plasmid Preparation, Sequencing, Software, In Silico, Microarray, Expressing