Project description:Non-coding RNA profiling by microarray in an Affymetrix® miRNA Array, version 4.1 (Santa Clara, CA, USA), commercially available by Thermo Fisher Scientific (Waltham, MA) We aimed to profile the expression of the entire population of annotated small non-coding RNAs in the Temporal Cortex (TC) of Alzheimer diseased (AD) individuals compared to age-matched controls.
Project description:The tumor suppressor CDKN2A Exon 1a (coding for p16) was removed in esophageal and squmous-columnar junction (SCJ) epithelial cells when tamoxifen was injected in experimental mice. Sections of the SCJ were subjected to laser capture microdissection to retain only the glandular mucosal layer. RNA was extracted and analyzed by Affymetrix Clariom D Pico assay, mouse (Thermo Fisher, Waltham, MA). We used microarrays to identify transcriptomic changes associated with p16 knockout.
Project description:To investigate the molecular pathological mechanisms of irritable bowel syndrome with diarrhea (IBS-D) and elucidate the effects of acupuncture on IBS-D colonic mucosa protein abundance in rats, a label-free high-throughput liquid chromatography-tandem mass spectrometry (LC-MS)-based proteomics analysis was used to survey the global changes of colonic mucosa proteins between different groups. A Nano flow Ultimate 3000 HPLC (Dionex Corp, Sunnyvale, CA) coupled online to a Q-Exactive Plus mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) was used in this project.
Project description:Genomic DNA was extracted from peripheral blood from patients with familial PD and their matched healthy siblings. Genomic microarray analysis of the subjects was performed using the CytoScan HD array platform. The CytoScan HD assay was performed according to the manufacturer’s protocol. CEL files that include the intensity probe signals were produced by GeneChip Scanner 3000 7G, using the GeneChip Command Console Software (Thermo Fisher Scientific, Waltham, MA, USA).
Project description:This study is a phase IV, randomized (1:1 ratio, blocks of various size, electronic allocation), open-label, active-controlled, multi-center trial enrolling adults aged sixty-five years or older to evaluate the different mechanisms of the immunological action of QIV-HD (Efluelda®) compared to QIV-SD (InfluvacTetra®). For transcriptomic analysis, 2.5 ml whole blood was collected in PAXgene tubes (Qiagen) from each subject before vaccination (D-7and D0) and 24 hours after (D1). Total RNA was extracted from blood according to the handbook of the PAXgene Blood RNA Kit. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set. One V2 sample (#02-066-FB) of QIV-SD group without good RNA quantity was removed for transcriptomic analyze. Sample preparation for microarray hybridization was carried out as described in the Applied BiosystemsTM GeneChipTM Whole Transcript (WT) PLUS Reagent Kit User Guide (Thermo Fisher Scientific, Waltham, MA, USA), and were hybridized to Applied BiosystemsTM GeneChipTM Clariom S human arrays. The fluorescent signals were measured with an Applied BiosystemsTM GeneChipTM GeneChip Scanner 3000 7G System, and controlled by the Applied BiosystemsTM GeneChipTM Command Console v5.0 software. Affymetrix’ Guanine Cytosine Count Normalization algorithm and Affymetrix’ Signal Space Transformation algorithm were used to normalized raw data by using Affymetrix Power Tools software v2.11.4. One V2 sample (#02-066-FB) of QIV-SD group without good RNA quantity was removed.
Project description:To explore the cellular pathways and the molecular functions affected by a novel biogenic amine, (3-HKA), we performed a label free quantitative (LFQ) proteomic analysis of mouse lymphatic endothelial cells (LEC), and primary dendritic cells, treated with IFNgammaplus or minus 3-HKA. Biological triplicates, of total cell lysates, were fractionated by one-dimensional gel electrophoresis (1DEF) and the “in gel” tryptic derived peptides analyzed by nano-LC-ESI-MS/MS on a Q Exactive HF quadrupole orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA). LFQ analysis highlighted that 3-HKA downregulated many of the inflammatory pathways, more notably JAK/STAT1 and NFkB, associated with IFNgamma activation.
Project description:Tandem Mass Tag (TMT) technology is an in vitro peptide labeling technique developed by Thermo Fisher Scientific, a peptide labeling technology developed in vitro. The technology uses six (TMTsixplex™ Isobaric Label Reagent Set) or 10 (TMT10plex™ Isobaric Label Reagent Set) isotope labels by labeling peptide specific amino acid sites. In TMT experiments, the relative and absolute amounts of proteins in up to 10 different samples can be compared flexibly by tandem mass spectrometry analysis. In TMT experiments, whole proteins from tissue cells are obtained by protein extraction, and the whole proteins are enzymatically cleaved into peptides by trypsin, and the TMT reagents are used to label all the obtained peptides. The TMT reagent consists of three main components: a reporter group, an equilibrium group and a peptide reaction group.
