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D.S. did most of the experimental procedures, and D. Gogendeau set up the SILAC experiments and performed the SILAC experiments including data analysis and the centrosome purifications.
SILAC experiments were carried out as described previously [45], [57].
SILAC ratios were determined using the ASAPRatio algorithm [32].
SILAC ratios for biotinylated and non-biotinylated proteins.
(A ) Design of the in vitro SILAC experiments.
For stable-isotope labeling by amino acids in cell culture (SILAC) experiments, the four cell lines were SILAC-labeled by culturing in DMEM/F-12 with the heavy isotope-labeled amino acids, (U-C6N4 -L-arginine U-C6N4 -L-arginine)-L-lysine (Lys-6) sU-C6N4 -L-arginine0% dialyzed fetal bovine serU-C6N4 -L-argininesolution, L-glutamine, SILAC phenol red solution, and penicillin-streptomycin.
For immunoblotting analyses we prepared biological replicates without SILAC and treated cells equally as in the SILAC experiment.
For SILAC quantitation, cells were pre-labeled by propagation in SILAC media and pooled prior to processing together.
Mass spectra were analyzed using MaxQuant software (version 1.0.0.7), which generates a peak list as well as SILAC- and extracted ion current-based quantitation for SILAC pairs.
SILAC-labelled mice have been described with near-complete labelling of all proteins, although the SILAC diet is expensive.
(D) Western blot validation of proteins identified by SILAC and LC-MS/MS.
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