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    Transnetyx algorithms image j nih
    Algorithms Image J Nih, supplied by Transnetyx, used in various techniques. Bioz Stars score: 99/100, based on 2191 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Article Title: Polyamine import and accumulation causes immunomodulation in macrophages engulfing apoptotic cells.
    Article Snippet: Origin Fetal Bovine Serum GeminiBio 100-500 5(6)-TAMRA,SE, mixed isomers Invitrogen C1171 Flash Red PS/DVB-COOH$(660,690) carboxyl polystyrene beads, 5mm Bangs Laboratories Inc. FCFR008 1-Palmitoyl-2-oleoyl-sn-glycero-3phospho-L-serine (POPS) Avanti Polar Lipids 840034P 1-palmitoyl-2-oleoyl-glycero-3phosphocholine (POPC) Avanti Polar Lipids 850457C HBSS Gibco 14175103 30% BSA Solution Sigma-Aldrich A8577 EDTA, pH 8.0 Invitrogen 15575020 Lipopolysaccharide, e-coli-O11:B4-derived (LPS) List Labs #201 Phosphate Buffered Saline, 1X (PBS) Gibco 20012027 0.5% Trypsin-EDTA, 10X Gibco 15400054 X-Vivo 10 Serum-free Hematopoietic Cell Medium Lonza 04-380Q Pooled human serum National Jewish Health N/A Cell-free amino acid mixture - 13C, 15N Sigma-Aldrich 767964 L-ARGININE:HCL (13C6, 99%; 15N4, 99%) Cambridge Isotope Laboratories CNLM-539-H-PK RPMI 1640 Medium for SILAC Thermo Scientific 88365 Fetal Bovine Serum - Dialyzed Sigma-Aldrich F0392 AMXT-1483 Aminex Therapeutics N/A Cytochalasin D Invitrogen PHZ1063 (Continued on next page) e1 Cell Reports 38, 110222, January 11, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER NSC23766 trihydrochloride Sigma-Aldrich SML0952 Wortmannin Sigma-Aldrich W1628 N(1)-Methylspermine nitrobenzoxadiazole conjugate 5 (NBD-Spermine) Aminex Therapeutics N/A Critical commercial assays FITC Annexin V Apoptosis Detection Kit I BD Pharmingen 556457 Deposited data Metabolomics data Metabolomics Workbench NMDR Project ID: PR001268 Experimental models: Cell lines Jurkat, clone E6-1 ATCC TIB-152 Experimental models: Organisms/strains C57BL/6J (WT) mice Jackson Labs 000664 CCR2KO mice Jackson Labs 004999 DsRed.T3 mice Nagy/Jackson Labs 006051 B6 CD45.1 mice Jackson Labs 002014 Oligonucleotides Taqman primers: il1b Applied Biosystems 4331182/Mm99999061_mH Taqman primers: il6 Applied Biosystems 4331182/ Mm00446190_m1 Taqman primers: b2m Applied Biosystems 4331182/ Mm00437762_m1 Software and algorithms Image J NIH https://imagej.nih.gov/ij/ FlowJo TreeStar Version 10 Prism GraphPad Version 7 Adobe Illustrator Adobe CC 2018 Other Genotyping service Transnetyx N/A ..



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    Figure 1. TGFb induces nuclear deformation, concomitant with defective nuclear lamina (A) Representative time-lapse images of A549 cells expressing GFP-H2B in the presence (+) or absence () of TGFb are shown. The alteration in the nuclear morphology became more evident 15 h after TGFb stimulation. The arrowheads indicate irregular nuclear shapes. Scale bars, 10 mm. (B) A549 cells were treated with (+) or without () TGFb for 72 h and stained for lamin A (green) and DNA (blue). The insets show a normal nucleus and two deformed nuclei classified as crumpling (a) or lobulation (b). Scale bars, 20 mm. (C) A549 cells were treated with TGFb for various times as indicated and stained for lamin A and DNA. The percentage of the cells with a crumpled or lobulated nucleus was measured (n R 339). (D) A549 cells were treated with TGFb for various times as indicated and stained for lamin A and DNA. The nuclear circularity (4p x area/perimeter2) of the cells was determined (n R 100). (E) Various cancer cell lines, as indicated, were treated with TGFb for 72 h and stained for lamin A and DNA. The percentage of the cells with a deformed nucleus was measured (n R 600). (F) A549 cells were treated with or without TGFb for 72 h and stained for lamin A. The line-scan profiles of lamin A at the selected region (as indicated by dashed lines) are shown using Zeiss Zen2 software. Scale bars, 10 mm. The percentage of the cells with apparent nucleoplasmic distribution of lamin A was measured (n R 246). (G) A549 cells were treated with or without TGFb for 72 h and solubilized in 1% NP40 lysis buffer. An equal proportion of cell lysates from the soluble and insoluble fractions was analyzed by immunoblotting with the antibodies as indicated. The

    Journal: iScience

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    doi: 10.1016/j.isci.2023.106992

    Figure Lengend Snippet: Figure 1. TGFb induces nuclear deformation, concomitant with defective nuclear lamina (A) Representative time-lapse images of A549 cells expressing GFP-H2B in the presence (+) or absence () of TGFb are shown. The alteration in the nuclear morphology became more evident 15 h after TGFb stimulation. The arrowheads indicate irregular nuclear shapes. Scale bars, 10 mm. (B) A549 cells were treated with (+) or without () TGFb for 72 h and stained for lamin A (green) and DNA (blue). The insets show a normal nucleus and two deformed nuclei classified as crumpling (a) or lobulation (b). Scale bars, 20 mm. (C) A549 cells were treated with TGFb for various times as indicated and stained for lamin A and DNA. The percentage of the cells with a crumpled or lobulated nucleus was measured (n R 339). (D) A549 cells were treated with TGFb for various times as indicated and stained for lamin A and DNA. The nuclear circularity (4p x area/perimeter2) of the cells was determined (n R 100). (E) Various cancer cell lines, as indicated, were treated with TGFb for 72 h and stained for lamin A and DNA. The percentage of the cells with a deformed nucleus was measured (n R 600). (F) A549 cells were treated with or without TGFb for 72 h and stained for lamin A. The line-scan profiles of lamin A at the selected region (as indicated by dashed lines) are shown using Zeiss Zen2 software. Scale bars, 10 mm. The percentage of the cells with apparent nucleoplasmic distribution of lamin A was measured (n R 246). (G) A549 cells were treated with or without TGFb for 72 h and solubilized in 1% NP40 lysis buffer. An equal proportion of cell lysates from the soluble and insoluble fractions was analyzed by immunoblotting with the antibodies as indicated. The

    Article Snippet: Plasmid: HA-Smad2 Addgene Cat#11734 Plasmid: FLAG-Smad3 Addgene Cat#11742 Plasmid: HA-AKT2 Addgene Cat#16000 Plasmid: HA-AKT1 Dr. Chi-Ying Huang (National YangMing Chiao Tung University) N/A Plasmid: FLAG-lamin A This paper N/A Plasmid: pMD.G National RNAi Core Facility (Academia Sinica) https://rnai.genmed.sinica.edu.tw/vector.html Plasmid: pCMV-DR8.91 National RNAi Core Facility (Academia Sinica) https://rnai.genmed.sinica.edu.tw/vector.html Plasmid: pLKO-AS1-puro National RNAi Core Facility (Academia Sinica) https://rnai.genmed.sinica.edu.tw/vector.html Software and algorithms ZEN2 software Carl Zeiss N/A Odyssey CLx Imaging System LI-COR Biosciences N/A Image J NIH https://imagej.nih.gov/ij/ EXCEL Microsoft N/A GraphPad Prism GraphPad https://www.graphpad.com/features Photoshop CS6 Adobe N/A Illustrator CS6 Adobe N/A

    Techniques: Expressing, Staining, Software, Lysis, Western Blot

    KEY RESOURCES TABLE

    Journal: Immunity

    Article Title: Programming of distinct chemokine-dependent and -independent search strategies for T helper-1 and Th2 cells optimizes function at inflamed sites

    doi: 10.1016/j.immuni.2019.06.026

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: Immunity, 15:303-311 ( 2001 ) N/A Mouse: B6.129S2(C)-Stat6 tm1Gru /J The Jackson Laboratory Stock No: 005977 Mouse: Albino B6 The Jackson Laboratory Stock No: 000058 Mouse: OTII TCR Transgenic B6 The Jackson Laboratory Stock No: 004194 Mouse: B6.129P2-Cxcr3tm1Dgen/J The Jackson Laboratory Stock No: 005796 Parasite: Leishmania Major strain WHOM/IR/-/173 R. Locksley (UCSF) N/A Oligonucleotides Integrin aL (CD11a), Itgal (Mm00801807_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin a1 (CD49a), Itga1 (Mm01306375_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin a2 (CD49b), Itga2 (Mm00434371_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin aV (CD51), Itgav (Mm00434486_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin b1 (CD29), Itgb1 (Mm01253230_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin b2 (CD18), Itgb2 (Mm00434513_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 Integrin b3 (CD61), Itgb3 (Mm00443980_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 T-bet, Tbx21 (Mm00450960_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 GATA-3, Gata3 (Mm00484683_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 GAPDH, Gapdh (Mm99999915_m1) Thermo Fisher (Applied Bioscience) Cat# 4331182 HPRT, Hprt (Mm00446968) Thermo Fisher (Applied Bioscience) Cat# 4331182 Software and Algorithms Velocity Software Perkin Elmer N/A Imaris Bitplane RRID:SCR_007370 Image J sofware NIH https://imagej.nih.gov/ij/ Flow Jo Tree Star RRID:SCR_008520 Prism 7 Graph Pad RRID:SCR_002798 Other Isoflurane vaporizer-ventilation machine Lei Medical Model# M3000R Olympus FVMPE-RS Olympus N/A Olympus FV-MRVGR/XR, filter set Olympus N/A 7900HT Fast Real-Time PCR System Applied Biosystems N/A FACSAria Cell Sorter BD Biosciences N/A BD LSR II BD Biosciences N/A FACSCalibur BD Biosciences N/A Open in a separate window KEY RESOURCES TABLE Differential dependency on chemokines for Th1 and Th2 cell interstitial migration Th differentiation programs elevated α V β 3 integrin expression on Th2 cells Increased α V β 3 integrin is sufficient to facilitate chemokine-independent migration Th1 and Th2 programming for distinct modes of migration optimizes effector function

    Techniques: Purification, Staining, Cell Culture, Virus, shRNA, Plasmid Preparation, Control, Recombinant, Adjuvant, Transgenic Assay, Software, Real-time Polymerase Chain Reaction