Journal: Developmental cell

Article Title: Nuclear scaling is coordinated among individual nuclei in multinucleated muscle fibers

doi: 10.1016/j.devcel.2019.02.020

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse anti-Lamin DHSB ADL67.10 Mouse anti-Fibrillarin1 EnCore MCA-38F3 Rabbit anti-H3K9ac Active Motif Catalog No: 39138 Mouse anti-Discs Large DHSB 4F3 Mouse anti-alpha tubulin Sigma DM1A Goat anti-mouse Alexa conjugated secondaries Life Technologies Experimental Models: Organisms/Strains D. melanogaster: w 1118 Bloomington Drosophila Stock Center BDSC:3605 D. melanogaster: DMef2-Gal4 Ranganayakulu et al., 1998 D. melanogaster: UAS-2×EGFP Bloomington Drosophila Stock Center BDSC:6874 D. melanogaster: UAS-GFP RNAi from J. Zallen (SKI) D. melanogaster: UAS-dMyc from N. Perrimon (HMS) D. melanogaster: UAS-dup (double parked/Cdt1) RNAi from T. Orr-Weaver (MIT) Software and Algorithms ImageJ/Fiji Fiji https://fiji.sc/ GraphPad Prism GraphPad https://www.graphpad.com/ Excel Microsoft https://products.office.com/en-us/excel Matlab Mathworks https://www.mathworks.com/products/matlab.html Imaris Bitplane http://www.bitplane.com/imaris/imaris R R Foundation for Statistical Computing https://www.r-project.org/ Cytosim Nédélec Laboratory http://github.com/nedelec/cytosim Illustrator Adobe www.adobe.com Open in a separate window KEY RESOURCES TABLE Muscle nuclei collectively establish precise global scaling with muscle fiber size Cells contain domains with distinct local scaling of DNA, nuclear and nucleolar sizes Nucleolar scaling indicates proportionally higher synthetic activity in small nuclei Changes in DNA content affect nuclear scaling relationships and muscle function

Techniques: Software

Journal: Cell reports methods

Article Title: Macrophage calcium reporter mice reveal immune cell communication in vitro and in vivo

doi: 10.1016/j.crmeth.2021.100132

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCES SOURCE IDENTIFIER Antibodies Ly6G - clone 1A8 BioLegend Cat #127616, RRID: AB_1877271 CD11b - clone M1/70 BioLegend Cat #101226, RRID: AB_830642 NK1.1 -clone PK 136 BioLegend Cat #108708 Thy1 - clone 53–2.1 BioLegend Cat #140307, RRID: AB_10643585 Ly6C - clone HK1.4 BioLegend Cat #128015, RRID AB_1732087 4′,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat #D1306 Ter119 - CD90.2 BioLegend Cat #116208, RRID: AB_313708 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 10X (PBS) Gibco 70011044 Bovine serum albumin (BSA) MP bio 160069 Red Blood Cell (RBC) Lysing Buffer 10X Invitrogen 50–112–9743 DMEM - Dulbecco’s Modified Eagle Medium (1X) Gibco 11965–092 DMEM - Dulbecco’s Modified Eagle Medium (1X) Gibco 31053–028 Opti-MEM Gibco 31985–070 FBS-Fetal Bovine Serum Corning 35010CV Penicillin-Streptomycin Solution, 100x Corning 30–002-CI Macrophage Colony-Stimulating Factor (Mcsf) Peprotech 315–02 Collagen type 1 Corning 354236 Lipofectamine 2000 agent Invitrogen 11668–030 Herring Testis (HT) DNA Sigma D6898 Experimental models: Organisms/strains Mouse: C57CL/6-Tg (Csf1r-cre)1Mnz/J Jackson Laboratory 029306 Mouse: B6;129S6-Polr2aTn (pb-CAG-GCaMP5g, -tdTomato) Tvrd Jackson Laboratory 024477 Software and algorithms FIJI National Institute of Health, USA RRID: SCR_002285 Matlab Mathworks R2020b Prism Graphpad Version 9.0 Flow cytometer sorter Sony MA900 FlowJo BDBiosciences N/A Other 35-mm glass dish Fluorodish fd35–100 MC38-H2B-mCherry colon cancer cell lines Center for Systems biology, Boston, MA N/A Fluoview FV1000 confocal microscope Olympus FV1000 Vivaview epifluorescence microscope Olympus LCV110U Dorsal skinfold chamber Custom-built N/A Isoflurane vetone fluriso 26675–46-7 Deposited Data Image and Signal Processing Code GitHub / Zenodo https://doi.org/10.5281/zenodo.5668359 Open in a separate window KEY RESOURCES TABLE A reporter mouse for measuring cellular calcium dynamics in macrophages Analysis pipeline infers cell-cell communication from correlated calcium dynamics Immune-stimulatory DNA promotes correlated calcium dynamics in vitro Spontaneous coordination between cells is detected in vivo MOTIVATION Macrophages contribute to diverse physiologic and pathogenic functions across every tissue in the body.

Techniques: Recombinant, Saline, Modification, Software, Flow Cytometry, Microscopy

Journal: Cell reports methods

Article Title: Macrophage calcium reporter mice reveal immune cell communication in vitro and in vivo

doi: 10.1016/j.crmeth.2021.100132

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCES SOURCE IDENTIFIER Antibodies Ly6G - clone 1A8 BioLegend Cat #127616, RRID: AB_1877271 CD11b - clone M1/70 BioLegend Cat #101226, RRID: AB_830642 NK1.1 -clone PK 136 BioLegend Cat #108708 Thy1 - clone 53–2.1 BioLegend Cat #140307, RRID: AB_10643585 Ly6C - clone HK1.4 BioLegend Cat #128015, RRID AB_1732087 4′,6-diamidino-2-phenylindole (DAPI) Invitrogen Cat #D1306 Ter119 - CD90.2 BioLegend Cat #116208, RRID: AB_313708 Chemicals, peptides, and recombinant proteins Phosphate-buffered saline 10X (PBS) Gibco 70011044 Bovine serum albumin (BSA) MP bio 160069 Red Blood Cell (RBC) Lysing Buffer 10X Invitrogen 50–112–9743 DMEM - Dulbecco’s Modified Eagle Medium (1X) Gibco 11965–092 DMEM - Dulbecco’s Modified Eagle Medium (1X) Gibco 31053–028 Opti-MEM Gibco 31985–070 FBS-Fetal Bovine Serum Corning 35010CV Penicillin-Streptomycin Solution, 100x Corning 30–002-CI Macrophage Colony-Stimulating Factor (Mcsf) Peprotech 315–02 Collagen type 1 Corning 354236 Lipofectamine 2000 agent Invitrogen 11668–030 Herring Testis (HT) DNA Sigma D6898 Experimental models: Organisms/strains Mouse: C57CL/6-Tg (Csf1r-cre)1Mnz/J Jackson Laboratory 029306 Mouse: B6;129S6-Polr2aTn (pb-CAG-GCaMP5g, -tdTomato) Tvrd Jackson Laboratory 024477 Software and algorithms FIJI National Institute of Health, USA RRID: SCR_002285 Matlab Mathworks R2020b Prism Graphpad Version 9.0 Flow cytometer sorter Sony MA900 FlowJo BDBiosciences N/A Other 35-mm glass dish Fluorodish fd35–100 MC38-H2B-mCherry colon cancer cell lines Center for Systems biology, Boston, MA N/A Fluoview FV1000 confocal microscope Olympus FV1000 Vivaview epifluorescence microscope Olympus LCV110U Dorsal skinfold chamber Custom-built N/A Isoflurane vetone fluriso 26675–46-7 Deposited Data Image and Signal Processing Code GitHub / Zenodo https://doi.org/10.5281/zenodo.5668359 Open in a separate window KEY RESOURCES TABLE A reporter mouse for measuring cellular calcium dynamics in macrophages Analysis pipeline infers cell-cell communication from correlated calcium dynamics Immune-stimulatory DNA promotes correlated calcium dynamics in vitro Spontaneous coordination between cells is detected in vivo MOTIVATION Macrophages contribute to diverse physiologic and pathogenic functions across every tissue in the body.

Techniques: Recombinant, Saline, Modification, Software, Flow Cytometry, Microscopy