Project description:Single-molecule read technologies allow for detection of epigenomic base modifications during routine sequencing by analysis of kinetic data during the reaction, including the duration between base incorporations at the elongation site (the "inter-pulse duration.") Methylome data associated with a closed de novo bacterial genome of Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 was produced and submitted to the Gene Expression Omnibus. Single-sample sequencing and base modification detection of cultured isolate of a foodborne pathogen.
Project description:We have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have measured the stutter patterns at various levels of PCR amplification during targeted amplification and library preparation processes
Project description:Single-molecule read technologies allow for detection of epigenomic base modifications during routine sequencing by analysis of kinetic data during the reaction, including the duration between base incorporations at the elongation site (the "inter-pulse duration.") Methylome data associated with a closed de novo bacterial genome of Salmonella enterica subsp. enterica serovar Javiana str. CFSAN001992 was produced and submitted to the Gene Expression Omnibus.
Project description:Objectives: To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). Methods: DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) genotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. The paternity testing parameters were attributed to each case quantitatively. Results: The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699-99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. Conclusions: Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.
Project description:Affymetrix Mouse Gene 1.0 ST Array profiles were generated from acticular cartilage derived from CBA and Str/ort mice at three ages (8W, 18W, 40W), corresponding to stages prior to, at and late after natural osteoarthritis (OA) onset in OA-prone Str/ort mice.
Project description:Affymetrix Mouse Gene 1.0 ST Array profiles were generated from acticular cartilage derived from CBA and Str/ort mice at three ages (8W, 18W, 40W), corresponding to stages prior to, at and late after natural osteoarthritis (OA) onset in OA-prone Str/ort mice. Two strains of mice, three ages, and three to four biological replicates.
Project description:P53 mutation is closely associated with the occurrence and progression of colon cancer. In this project, we did crotonylomics sequencing by using human colon cancer homologous cell line pair-HCT116+/+(with wild type p53) and HCT116-/- (with null p53). Crotonylomics sequencing results showed that p53 deficiency regulated crotonylation of non-histone proteins.
