Project description:Protein extract from symbiontic Burkholderia Kirkii (3 replicates: A,B,C): each fractionated by SDS-PAGE and digested using Trypsin, each fraction measured twice in LC-MSMS, once in discovery mode and once using an exclusion list based on first run. Mass spectra were searched against a protein sequence database containing products of both predicted protein coding genes and pseudogenes for B. kirkii, genes predicted by the Prodigal software, genes predicted by in-house software, P. kirkii chloroplastic proteins, as well as protein sequences of 256 common contaminants. We used Mascot search engine (version 2.3.0) with the following search parameters: Carbamidomethylation was set as a fixed modification on all Cysteines, oxidation of Methionines, deamidation of Asparagines and Glutamines, as well as cyclization of N-terminal Glutamines were considered as optional modifications. Precursor ion mass tolerance was set to 10 ppm, fragment ion mass tolerance was set to 0.8 Da, and the automatic decoy search option was enabled. Spectra were searched for a match to fully-tryptic and semi-tryptic peptides with up to two missed cleavage sites. The built-in version of Mascot Percolator was used to improve the peptide spectrum match (PSM) scores. Peptides were assessed with the PeptideClassifier software. Additional genome annotation is held at ENA under the accession: WGS project CAFE00000000.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..