Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs. Examination of transcription start sites by biological duplicates from E. coli and K. pneumoniae
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs.
Project description:Topo IV cleavage sites induced by ciprofloxacin were identified in the E. coli genome with a single-nucleotide resolution using Topo-Seq.
Project description:Cleavage sites induced by the EcTopoI G116S M320V topoisomerase mutant were identified in E. coli genome with a single-nucleotide resolution using Topo-Seq.
Project description:Using ChIP-exo, we have identified at single nucleotide resolution genomic binding sites for UvrY in E. coli and its homolog SirA in S. Typhimurium.
Project description:Illumina whole genome SNP (single nucleotide polymorphism) microarray analysis was carried out on the patient in order to determine copy number variations and to assess their disease etiopathogenesis.
