imagej’s jacop plugin version 2006/05/31  (Institut Curie)

Journal: Cellular & Molecular Biology Letters

Article Title: Golgi-associated retrograde protein (GARP) complex-dependent endosomes to trans Golgi network retrograde trafficking is controlled by Rab4b

doi: 10.1186/s11658-024-00574-w

Figure Lengend Snippet: Inactive Rab4b blocks retrograde trafficking to the TGN. A Western blots of Rab4b on lysates prepared from cells transfected with (ctrl: 30 nM) or anti-Rab4b siRNA (5, 30 nM) as described in . Quantification of Rab4b mRNA expression in cells treated with 20 nM ctrl or anti-Rab4b siRNA. B Western blot of sortilin as in Fig. A from control- or Rab4b siRNA-treated cells, and quantification of 3 experiments. *, p < 0.05 (two-way ANOVA). ( C ) Western blots of CI-M6PR, sortilin, and tubulin as loading control from controlor Rab4b siRNA-treated cells incubated without or with leupeptin and E64 and the quantification of 3 independent experiments. Significance compared to the ctrl/no leu/E64 condition with * p < 0.05, ** p < 0.01, *** p < 0.001; significance compared with the Ctrl within the condition no leu/E64 and leu/E64 # p < 0.05 (one-way ANOVA). D Western blots of sortilin, and tubulin as loading control, from control or Rab4b siRNA treated wt cells or Rab4b overexpressing cells. E Quantification of the percentage of iCD8-M6PR at the Golgi in randomly acquired whole fields in control- or Rab4b siRNA-treated cells using the protocol 1 (Additional file : Fig. S2A). F I colocalization index (RColoc) between iCD8-CI-M6PR and Golgi, or iCD8-CI-M6PR and co-internalized Tf, determined in the same experiments as in E, using the colocalization plugin of the open ImageJ software . G Quantification the percentage of iCD8-M6PR at the Golgi in randomly acquired whole fields in control- or Rab4b siRNA-treated cells using the protocol 2 (Additional file : Fig. S2A) and representative images on the left panel. H Quantification of iCD8-M6PR in the Golgi of single cells overexpressing HA-Rab4b S22N (red star marks) and in the surrounding non-transfected cells (NT) and representative images according to protocol 1 (Additional file : Fig. S2A). E–H Significance compared to siRNA ctrl condition with *p < 0.05, **p < 0.01, ****p < 0.0001 (Student t test). Bars are for 10 µm

Article Snippet: Co-localization indexes were determined using the JACoP plugin or Imaris (OXFORD Instruments).

Techniques: Western Blot, Transfection, Expressing, Control, Incubation, Software

Journal: iScience

Article Title: Circ-Hdgfrp3 shuttles along neurites and is trapped in aggregates formed by ALS-associated mutant FUS

doi: 10.1016/j.isci.2021.103504

Figure Lengend Snippet: Key resources table

Article Snippet: ImageJ “JACoP (Just Another Colocalization Plugin)” plugin , Fabrice P. Cordelieres, Institut Curie, Orsay (France)( Bolte and Cordelières., 2006 ) , https://imagej.nih.gov/ij/plugins/track/jacop.html.

Techniques: Transduction, Virus, Recombinant, Electron Microscopy, Sterility, Modification, Knock-Out, Transfection, RNAscope, Cloning, Mutagenesis, Expressing, Sequencing, Plasmid Preparation, Negative Control, Software, Real-time Polymerase Chain Reaction, Microscopy

Journal: Cancer letters

Article Title: Tyrosine phosphorylation of HSC70 and its interaction with RFC mediates methotrexate resistance in murine L1210 leukemia cells

doi: 10.1016/j.canlet.2014.11.036

Figure Lengend Snippet: Colocalization of HSC70 and RFC in L1210/0 and L1210/DDP cells. (A) HSC70 expression, RFC expression, and overlay (merged) image of HSC70 and RFC channels (specific wave lengths of fluorescent light) in L1210/0 cells with or without MTX. (B) HSC70 expression, RFC expression, and overlay (merged) image of HSC70 and RFC channels in L1210/DDP cells with or without MTX. The yellow fluorescence represents the expression of HSC70 immuno-tagged with alexa fluor 546. The red fluorescence represents the expression of RFC immune-tagged with alexa fluor 647. The images were captured with confocal laser scanning microscopy at 60× objective, 1024 resolution and 2.1 optical zoom and turned to 8-bit color and analyzed for colocalization using JACoP plugin from image J. The images shown are representative of three independent experiments. (C) 2D scatter plot colocalization of L1210/0 cells and L1210/DDP cells with or without MTX. The yellow channel (Alexa Fluor 546) for HSC70 is graphed along the X-axis and the red channel for RFC (Alexa Fluor 647) is plotted on the Y-axis. The plots shown are a representation of three independent experiments. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The fluorescent emissions were quantified using NIH software imageJ plugin JACoP and Olympus Fluoview 1000 (Olympus, Center Valley, PA, USA).

Techniques: Expressing, Fluorescence, Confocal Laser Scanning Microscopy