Project description:To explore the protein components for scallop byssus, the soluble fractions of scallop byssus was extract. For mass spectrometric analysis, proteins were extracted from byssal adhesive plaques, and the whole protein smple was treated with trypsin and analyzed using Thermo Fisher Q Exactive Mass Spectrometer (Thermo Fisher Scientific, USA). The mass spectrometry raw data were searched against the full set of predicted proteins from the C. farreri genome and Transcriptome using Mascot v2.3.0 (Matrix Science, London, UK).
Project description:M. hominis cells were grown in liquid medium supplied with arginine or thymidine as a carbon source. LC-MS analysis was performed on Ultimate 3000 Nano LC System (Thermo Fisher Scientific) coupled with Q Exactive HF benchtop Orbitrap mass spectrometer (Thermo Fisher Scientific) via a nanoelectrospray source (Thermo Fisher Scientific), an untargeted label-free bottom-up proteomic strategy was used, DDA (Data Dependent Acquisition) approach. Protein identification and label-free quantification were performed with PEAKS software.
Project description:LC-MS/MS identification of small subunit peptides of Photosystem II assembly intermediate (NRC) with/without trypsin digestion. Peptide sequence identification with HCD fragmentation using Q-Exactive plus mass spectrometer (Thermo-Fisher)
Project description:This study examined microRNA expression of cells maintained in media prepared with replete serum (EVR) or with serum depleted of extracellular vesicles (EVs) by either of two methods: standard overnight ultracentrifugation (UC-EVD) or a proprietary method used by Thermo Fisher (TF-EVD).
Project description:HEK293T cells were ectopically expressing Flag tagged p62 (p62 group) or empty vectors (Control group) for 48h, cell lysates were incubated with anti-Flag affinity gels, and co-immunoprecipitates were subjected to trypsin digestion followed by mass spectrometry analysis. Peptides were separated by the EASY-nLC system (Thermo Fisher) and analyzed by the Q Exactive mass spectrometer (Thermo Fisher). Protein analysis were performed with Thermo Proteome Discoverer 2.1 (Thermo Fisher) and searched against Uniprot Human database. Three samples per group.
Project description:HEK293T cells were ectopically expressing Flag tagged p62 (p62 group) or empty vectors (Control group) for 48h, cell lysates were incubated with anti-Flag affinity gels, and co-immunoprecipitates were subjected to trypsin digestion followed by mass spectrometry analysis. Peptides were separated by the EASY-nLC system (Thermo Fisher) and analyzed by the Q Exactive mass spectrometer (Thermo Fisher). Protein analysis were performed with Thermo Proteome Discoverer 2.1 (Thermo Fisher) and searched against Uniprot Human database. Three samples per group.
Project description:In this project, Q-Exactive HF(Thermo Fisher Scientific,San Jose,CA) was used to acquire mass spectrometry (MS) data for 7 samples in Data Independent Acquisition (DIA) mode. Quantification of peptides and proteins was performed using Spectronaut™ and MSstats software packages
Project description:We aimed to identify urinary exosomal miRNAs associated with PCa metastasis and develop a non-invasive risk-scoring model for PCa metastasis in this study. MiRNA profiles were examined using the Taqman low-density miRNA array (TLDA). Megaplex reverse transcription reactions and pre-amplification reactions were performed to increase the quantity of cDNA for miRNA expression analysis using the Megaplex PreAmp Primers Human Pool A and TaqMan PreAmp Master Mix (Thermo Fisher Scientific). MiRNA expression was evaluated via the TLDA panel A v2.0 (Thermo Fisher Scientific). Raw data were processed using the QuantStudio Real-Time PCR Software (Thermo Fisher Scientific) to determine a cycle threshold (Ct) value for each miRNA.
Project description:We extracted RNA of sorted lung SPC/GFP+ EpCAM+ cells and performed microarray analyses. Total RNA was extracted from sorted Ep-CAMhigh/GFPhigh cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The RNA integrity was examined on an Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA). Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix/Thermo Fisher Scientific). Fragmented and labeled ss-cDNA were hybridized on a GeneChip Clariom S Array (Affymetrix/Thermo Fisher Scientific) (n =3/group). We used microarrays to detail the global gene expression of SPC/GFP+ EpCAM+ cells from the control mice(G29-5_(Clariom_S_Mouse)) and the 3 months smoke mice(G29-6_(Clariom_S_Mouse)), and identified distinct classes of up-regulated genes during this process.