algorithms image j nih  (Transnetyx)

Journal: iScience

Article Title: AKT2-mediated nuclear deformation leads to genome instability during epithelial-mesenchymal transition.

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

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