Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures. Hybridizations used NimbleGen expression array chips (Product no. A4385-00-01, platform accession no GPL15883) designed against the 5,657 ORFs encoded in the A. variabilis genome (GenBank accession no. CP000117). Each ORF was represented by seventeen 60-mer oligonucleotides. Each oligonucleotide was present in four internal replicates. The twenty-seven microarray data files were normalized against each other. Expression array data were analyzed using ArrayStar 3.0 (DNASTAR, Madison, WI).
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