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PROVIDER: PRJNA616006 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
2012-08-30 | GSE39667 | GEO
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
2012-08-30 | E-GEOD-39667 | biostudies-arrayexpress
Project description:Genome sequence of Escherichia coli clinical strains
| PRJNA622815 | ENA
Project description:Escherichia coli strain C is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. We found that E. coli C forms more robust biofilms than the other four laboratory strains. Here we present the complete genomic sequence of this strain in which we utilized high resolution optical mapping to confirm a large inversion in comparison to other strains. DNA sequence comparison revealed the absence of several genes involved in biofilm formation, such as antigen 43, waaSBOJYZUL for LPS synthesis, and cpsB for curli synthesis. The main difference affecting biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the -35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. Analysis of gene expression profiles in planktonic and biofilm attached cells by the RNAseq method allows better understanding of this regulatory pathway in E. coli.
2020-01-01 | GSE125110 | GEO
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.
2017-06-21 | GSE89685 | GEO
Project description:We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains
2016-12-13 | GSE92255 | GEO
Project description:Background Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all serotypes. Results For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames, with a mean number of 729 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. Conclusion These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships. Keywords: comparative genomic hybridization
2007-07-01 | GSE5212 | GEO
Project description:Escherichia coli strains producing exogenous internal membrane proteins
2019-02-27 | GSE109819 | GEO
Project description:Archer2011 - Genome-scale metabolic model of
Escherichia coli (iCA1273)
This model is described in the article:
The genome sequence of E.
coli W (ATCC 9637): comparative genome analysis and an improved
genome-scale reconstruction of E. coli.
Archer CT, Kim JF, Jeong H, Park JH,
Vickers CE, Lee SY, Nielsen LK.
BMC Genomics 2011; 12: 9
Abstract:
BACKGROUND: Escherichia coli is a model prokaryote, an
important pathogen, and a key organism for industrial
biotechnology. E. coli W (ATCC 9637), one of four strains
designated as safe for laboratory purposes, has not been
sequenced. E. coli W is a fast-growing strain and is the only
safe strain that can utilize sucrose as a carbon source.
Lifecycle analysis has demonstrated that sucrose from sugarcane
is a preferred carbon source for industrial bioprocesses.
RESULTS: We have sequenced and annotated the genome of E. coli
W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two
plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also
present. W has unique features relative to other sequenced
laboratory strains (K-12, B and Crooks): it has a larger genome
and belongs to phylogroup B1 rather than A. W also grows on a
much broader range of carbon sources than does K-12. A
genome-scale reconstruction was developed and validated in
order to interrogate metabolic properties. CONCLUSIONS: The
genome of W is more similar to commensal and pathogenic B1
strains than phylogroup A strains, and therefore has greater
utility for comparative analyses with these strains. W should
therefore be the strain of choice, or 'type strain' for group
B1 comparative analyses. The genome annotation and tools
created here are expected to allow further utilization and
development of E. coli W as an industrial organism for
sucrose-based bioprocesses. Refinements in our E. coli
metabolic reconstruction allow it to more accurately define E.
coli metabolism relative to previous models.
This model is hosted on
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MODEL1507180010.
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2015-07-30 | MODEL1507180010 | BioModels
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.
2019-05-31 | GSE110005 | GEO