Project description:The specificity of the RNA-CASing process was analysed by Next-Generation Sequencing. Therfor small RNAs were isolated from purified proteins of Escherichia coli and subjected to Illumina sequencing or nanopore sequencing.
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
Project description:The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here, microarray from GSE48776). mRNA profiles of Wild Type and two Mutant Strains (ydcR (b1439) MUTANT and yjiR (b4340) MUTANT), growth in minimal medium, were generated by deep sequencing, in triplicate, using Illumina MiSeq.
Project description:S. meliloti strains with a bi- and monopartite genome configuration were constructed by consecutive Cre/lox-mediated site-specific fusions of the secondary replicons. Beside the correct genomic arrangements, these strains and precursors were tested for variations in the nucleotide sequence. Futher, a marker fequency analysis was performed to test if replication is initiated at all origins and to determine the replication termination regions of the triple replicon fusion molecule. To gain the sequence data for these analyses, respective strains were applied to whole genome sequencing using an Illumina MiSeq-System and Oxford Nanopore (MinION) sequencing technology.
Project description:A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3 was isolated from a system of alkaline soda lakes in the Kulunda Steppe. Its complete, circular genome was assembled from combined nanopore and illumina sequencing and its proteome was determined for three different experimental conditions: growth on Staphylococcus cells, casein, or peptone. AB-CW3 is an aerobic bacterium feeding mainly on proteins and peptides.
Project description:Purpose: The identification of genes and regulatory pathways by OxyS sRNA in Escherichia coli. Methods: mRNA profiles of OxyS overexpression in wild-type and knockout of hfq strains using Illumina sequencing. Ribosomal RNA depletion from total RNA was performed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Illumina) according to manufacturer protocols. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) by the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using a pair-end 50 bp sequencing. The sequence data for the reference genome (E. coli K-12 MG1655) was retrieved from the NCBI database. Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2 software. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM). All data processing were further performed by CLRNASeq V.1.00 (Chunlab, South Korea). Results: Using an optimized data analysis workflow, about 1 million sequence reads per sample to the E. coli K-12 genome were mapped and identified 4,224 and 4,303 transcripts in wild-type and hfq- strains, respectively. After TMM (Trimmed Mean of M-value) normalization and elmination of <100 reads in control and OxyS overexpression, 3,524 or 2,748 genes in hfq+ or hfq- strain, respetively, were utilized as a set to screening of candidates related to OxyS phenotype. Conclusions: Our study represents the first detailed analysis of OxyS transcriptomes in hfq+ and hfq- strains, generated by RNA-seq technology. The optimized data analysis workflows reported here could comparative investigate the expression profiles of sRNA in different background strains. We conclude that RNA-seq based transcriptome characterization of sRNAs would unravel genetic network in complex biologic functions.
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison
Project description:We investigated the gene expression changed in the NCM3722 wild-type and gcvB deletion strains grown in glucose minimal medium, aiming to find novel target genes controlled by small RNA GcvB. In total, five differentially expressed genes (DEGs) were identified by Illumina sequencing using a cutoff with fold change>2 and q-value<0.01. Following physiological and molecular studies identified that the physiological roles of GcvB were beyond amino acids transportation and it regulates oxdative stress response of Escherichia coli through its control of OxyR.