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The cell proliferation was tested using the Cell Counting Kit-8 (CCK-8, Dojindo, Japan) according to the manufacturer's instructions with slight modification (Eike et al. 2015).
IHC staining was performed according to the manufacturer's instructions with slight modifications.
For HTS experiments, total RNA was treated with the MICROBExpress kit (Ambion) to limit contamination by multicopy structural rRNAs, following manufacturer's instructions with slight modifications.
Plasma samples and amino acid calibration standards were prepared with MassTrak Amino Acid Analysis Solution (AAA) kit from Waters according to instructions with slight modifications for detection on a mass spectrometer.
Briefly, DNA was extracted using the Qiagen Blood and Tissue kit following the manufacturer's instructions with slight modifications (after step 3, we added an incubation time of 10 minutes at 70°C).
ELISAs were performed according to manufacturer's instructions with slight modifications.
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The phosphopeptides from digested peptides were enriched by using Phosphopeptide Enrichment TiO2 Kit (Calbiochem, San Diego, CA) according to the manufacturer's instruction with slight modifications.
Hydroxyproline content was measured using hydroxyproline assay kit from Biovision (Milpitas, CA) according to the manufacture's instruction with slight modification.
DNA extraction was carried out using the Plant Nucleospin II Kit (Macherey & Nagel, Düren, Germany) following manufacture's instruction with slight modifications according to Lucas et al. [ 21].
All of the eluted peptide fractions were concentrated with a vacuum centrifuge and solubilized in 200 μl TiO2 phosphobind buffer containing 50 g/L 2,5-dihydroxybenzoic acid for subsequent phosphopeptide enrichment using a Phosphopeptide Enrichment TiO2 kit (Calbiochem, San Diego, CA) according to the manufacturer's instruction with slight modifications.
The in situ proximity ligation assay (PLA), Duolink™, was from Olink Bioscience (Uppsala, Sweden) and performed according to the manufacturer's instructions [42], with slight modifications.
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