mRNA was isolated from MSC-derived EVs using the mirVana PARIS total RNA isolation kit (Life Technologies) according to the manufacturer’s protocol. mRNA sequencing was performed at the Mayo Clinic Bioinformatic Core, as previously described13 (link). Samples were sequenced on an Illumina HiSeq 2000 using TruSeq SBS kit version 3 and HCS v2.0.12 data collection software and data analyzed using the MAPRSeq v.1.2.1 system and the Bioinformatics Core standard tool, which includes alignment with TopHat 2.0.627 (link),28 (link) and gene counts with the featureCounts software29 (link). Normalized expression values for each gene were calculated as reads per kilobase per million (RPKM).
In addition, liquid chromatography mass spectrometry (LC-MS/MS) proteomic analysis was performed as previously described30 (link),31 (link). EV pellets were solubilized and lysed, and protein samples denatured. Aliquots were resolubilized in reducing sample buffer and samples electrophoresed. Gel sections were digested with trypsin31 (link), and peptides extracted and transferred onto a PicoFrit column 9 (NewObjective), self-packed with Agilent Poroshell 120 S 2.7 µm EC-C18 stationary phase, using a Dionex UltiMate 3000 RSLC LC system (Thermo-Fisher Scientific). Peptides were separated and eluting peptides analyzed using a QExactive mass spectrometer (Thermo-Fisher Scientific).
In addition, liquid chromatography mass spectrometry (LC-MS/MS) proteomic analysis was performed as previously described30 (link),31 (link). EV pellets were solubilized and lysed, and protein samples denatured. Aliquots were resolubilized in reducing sample buffer and samples electrophoresed. Gel sections were digested with trypsin31 (link), and peptides extracted and transferred onto a PicoFrit column 9 (NewObjective), self-packed with Agilent Poroshell 120 S 2.7 µm EC-C18 stationary phase, using a Dionex UltiMate 3000 RSLC LC system (Thermo-Fisher Scientific). Peptides were separated and eluting peptides analyzed using a QExactive mass spectrometer (Thermo-Fisher Scientific).
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