Project description:Roles of mesothelial cells (MCs) are poorly understood during liver development and injury. We identified podoplanin (Pdpn) as a cell surface markers for mesothelial cells in E12.5 mouse developing liver. To identify genes uniquely expressed in MCs, we isolated MCs from E12.5 mouse livers by FACS using anti-Pdpn antibodies and performed microarray analysis. The E12.5 liver was digested with trypsin-EDTA and incubated with antibodies against Pdpn. MCs were isolated as Pdpn+ population by FACS. Total RNA was extracted with RNAqueous Micro (Ambion) and the probes for the microarray were synthesized using the Ovation RNA amplification system V2 and FL-Ovation cDNA Biotin module V2 (Nugen). The labeled probes were hybridized with GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) and signals were analyzed with Genomic Suite software (Partek).
Project description:This is the first report of a bacteriocin being produced by lactobacillus acidophilus ATCC 4356. For protein identification, the ~8-kDa peptide band was removed from the acrylamide gel and digested in-gel by trypsin, and the resulting peptide fragments were extracted and analyzed by LC-MS/MS analysis. The MS data were processed using Thermo Proteome Discoverer software (v2.2) with the SEQUEST search engine. Three peptides, VAHCASQIGR (amino acids 23-32), GSAACVSYLTR (amino acids 69-79), GSAACVSYLTRHRHH (amino acids 69-83) were identified as tryptic fragments on the basis of LC-MS/MS.This is the first report of a bacteriocin being produced by lactobacillus acidophilus ATCC 4356. For protein identification, the ~8-kDa peptide band was removed from the acrylamide gel and digested in-gel by trypsin, and the resulting peptide fragments were extracted and analyzed by LC-MS/MS analysis. The MS data were processed using Thermo Proteome Discoverer software (v2.2) with the SEQUEST search engine. Three peptides, VAHCASQIGR (amino acids 23-32), GSAACVSYLTR (amino acids 69-79), GSAACVSYLTRHRHH (amino acids 69-83) were identified as tryptic fragments on the basis of LC-MS/MS.
Project description:Mouse hippocampus membrane fractions were prepared using sucrose density gradient ultracentrifugation. Membrane proteins were solubilized using three different condition; 6-ACA/Triton X-100 or ProteoExtract Native Membrane Protein Extraction Kit (Calbiochem, Cat. No. 444810) or ProteoExtract Transmembrane Protein Extraction Kit (Novagen, Cat. No. 71772-3). Solubilized membrane proteins were separated on Blue Native PAGE or SDS-PAGE. Protein bands were excised, destained for peptide sample preparation. Proteins were reduced (DTT), alkylated (iodoacetamide), and in-gel digested with chymotrypsin or trypsin. Digested peptides were extracted then subjected to nanoHPLC and tandem MS analysis with Thermo Orbitrap Velos Pro mass spectrometer.
Project description:Three individual patient-originated (Scalp trauma; ages 37, 46 and 57) DPCs were used for the studies. Dermal papilla cells, derived from the frontal scalp of 3 women, were treated with normal medium (Ctrl group) and medium containing 10-7 M corticotropin-releasing hormone (CRH group) for 72 h. Proteins were extracted and digested with trypsin for 4D label-free quantitative proteomics (Shanghai Applied Protein Technology Co., Ltd.).
Project description:Klebsiella pneumoniae is an important opportunistic pathogen associated with multidrug-resistant infections in humans and animals. In this study, we performed a global proteomic analysis of the isolate JX21CTR26 to characterize its whole-cell protein expression profile. Bacterial cells were cultured under standard laboratory conditions, and total proteins were extracted, digested with trypsin, and analyzed by high-resolution LC–MS/MS. The resulting dataset provides a comprehensive catalog of proteins expressed by K. pneumoniae JX21CTR26 and a resource for further studies on antimicrobial resistance and virulence mechanisms in this strain.
Project description:<p> This study employs yeast as a model system to thoroughly investigate the differences in regulatory mechanisms under various nutrient limitation conditions, utilizing a systems biology approach integrated with techniques such as multi-omics analysis.To obtain a comprehensive quantitative landscape of protein expression in (human lung adenocarcinoma), we performed TMT 6-plex–based comparative proteomic analysis. Tumour and adjacent non-tumour tissues (n = 6 pairs) were pulverised under liquid nitrogen and total proteins extracted by phenol–ammonium acetate/methanol precipitation. After reduction, alkylation and acetone precipitation, 50 µg proteins per sample were digested in-solution with trypsin (1:50, w/w, 37 °C, 16 h). Peptides were labelled with TMT 6-plex reagents, pooled and fractionated by high-pH reversed-phase chromatography on an Agilent 1100 HPLC (Zorbax Extend-C18, 15 fractions). LC-MS/MS was carried out on a Q Exactive HF-X (Thermo) in DDA mode. Quantitative analysis was performed with Proteome Discoverer 2.4 using a 1 % FDR threshold at PSM and protein levels. The dataset provides relative abundance information for > 6 000 protein groups across tumour and control tissues, serving as a resource for biomarker and pathway studies in lung adenocarcinoma. </p>
Project description:The experiment aimed to study the proteome variation in a yeast strain (YS031), which chromosome II was artificially synthezied, compared with the wild type strain (BY4741). Proteins were extracted from the yeast cells and digested with trypsin. The peptides were label with iTRAQ, separated with 2D LC (SCX and RP) and detected with a Q-Exactive MS. Proteome identification and quantification were performed with Mascot2.3 and iQuant3.0.
Project description:Femur and Tibia of Mice 3 months of age were dissected, growth plate removed, and serial digested with collagenase-trypsin to remove endosteal and periosteal cells. The cortical bone tubes, highly enriched in osteocye in their natural bone matrix environment where then cultured with and and with out PTH at 250nM for 24hr, RNA extracted and biotinylated cDNA prepared, and hybrized to Illumina MouseWG-6_V2 arrays. Data was analyzed using Genome Studio-Gene Expression Module from Illumina.
Project description:Escherichia coli is an important opportunistic pathogen associated with multidrug-resistant infections in humans and animals. In this study, we performed a global proteomic analysis of the isolateEC15 to characterize its whole-cell protein expression profile. Bacterial cells were cultured under standard laboratory conditions, and total proteins were extracted, digested with trypsin, and analyzed by high-resolution LC–MS/MS. The resulting dataset provides a comprehensive catalog of proteins expressed by Escherichia coli EC15 and a resource for further studies on antimicrobial resistance and virulence mechanisms in this strain.