Computational protocol: Dendritic Cell-Mediated Phagocytosis but Not Immune Activation Is Enhanced by Plasmin

Similar protocols

Protocol publication

[…] Phase-contrast micrographs were taken with a Leica DM-IRB microscope. Camera: Hamamatsu ORCA-AG. Objective: NPLAN 40x, 0.55 NA. Acquisition software was MetaMorph v.7.5 (Molecular Devices, Sunnyvale, CA, USA). Images were processed with ImageJ v.1.42q (National Institute of Health). Confocal micrographs were taken on a Nikon A1r-si resonant scanning confocal system (microscope: Nikon Ti; objective: Apo LWD, 40x magnification, 1.15 numerical aperture, water immersion; sequential excitation: 405 nm, 488 nm and 546 nm laser lines; respective emission filters: 450/50 nm, 525/50 nm and 595/50 nm; photomultiplier tube detectors; acquisition software: NIS elements Advanced Research). Images were processed with ImageJ v.1.47q (National Institute of Health). [...] MoDCs were incubated in the presence/absence of 100 nM plasmin. After 3 hours of incubation, cell homogenates were prepared and sent to Kinexus Bioinformatics (Vancouver, BC, Canada) for blinded kinomic analysis using the KAM-1.2 chip equipped with ~500 pan-specific and ~300 phospho-site specific antibodies as previously described []. The short list of differentially regulated events identified by the KAM-1.2 chip was subjected to two independent forms of computational pathway analyses: the first was via Ingenuity Pathway Analysis where the analyst (from the Australian Proteome Analysis Facility) was blinded to both the experimental design and the overall project hypothesis, the second was a batch enquiry of the US National Cancer Institute/Nature Publishing Group-curated Pathway Interaction Database []. […]

Pipeline specifications

Software tools IPA, PID
Application Protein interaction analysis
Organisms Mus musculus, Homo sapiens
Diseases Autoimmune Diseases, Carcinoma, Renal Cell