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Analysis of Chromosome VIII of EC-C1 strains (S. cerevisiae)

ABSTRACT: The genomic DNA of rearranged chromosome VIII (~900kb) of EC9 diploid strain was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify it's amplified regions

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE38034 | GEO | 2012/05/18

SECONDARY ACCESSION(S): PRJNA167120

REPOSITORIES: GEO

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Analysis of Chromosome VIII of EC-C1 strains (S. cerevisiae)

Project description:The genomic DNA of rearranged chromosome VIII (~900kb) of EC9 diploid strain was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify it's amplified regions After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit for Array-comparative genomic hybridization.

2012-05-17 | E-GEOD-38034 | biostudies-arrayexpress

Analysing of Chromosome VIII of EC9-7 after experimental evolution (S. cerevisiae)

2011-11-13 | GSE33652 | GEO

Analysing of Chromosome VIII of EC9-7 after experimental evolution (S. cerevisiae)

Project description:The genomic DNA of wild-type chromosome VIII of evolved EC9-7 cells was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify its chromosomal composition Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit. After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.

2011-11-13 | E-GEOD-33652 | biostudies-arrayexpress

Comparative genomic hybridization of B. pertussis chromosomal fragments separated by PFGE

Project description:The genomes of Bordetella pertussis strains with different passage histories were digested with a restriction endonuclease and separated by pulsed-field gel electrophoresis (PFGE). Each PFGE fragment was labeled and hybridized to a microarray to assess the genome content of the fragment.

2006-04-30 | E-TABM-58 | biostudies-arrayexpress

Transcription profiling of 61 Salmonella enterica serovar Typhimurium isoltates to identify hotspots in genome variation and distinguish between different isolates from the same geographical region

Project description:A collection of 61 Salmonella enterica serovar Typhimurium (S. Typhimurium) of animal and human origin, matched as closely as possible by phage type, antimicrobial resistance pattern and place / time of isolation, and sourced from farms or hospitals in Scotland, were analysed by antimicrobial susceptibility testing, phage typing, pulsed field gel electrophoresis (PFGE), plasmid profiling and DNA microarrays. PFGE of all 61 isolates revealed ten PFGE profiles, which clustered by phage type and antibiotic resistance pattern, with human and animal isolates distributed between PFGE profiles. Analysis of 23 representative S. Typhimurium strains hybridised to a composite Salmonella DNA microarray identified a small number of specific regions of genome variation between different phage types and PFGE profiles. These variable regions of DNA were typically located within prophage-like elements. Simple PCR assays were subsequently designed to discriminate between different isolates from the same geographical region.

2007-06-09 | E-SGRP-6 | biostudies-arrayexpress

Determining genetic stability in Clostridium tetani vaccine strains

Project description:To develop a method for improved assessment of the genetic stability of bacterial vaccine strains, we applied next-generation sequencing to a Clostridium tetani model strain (including inter- and intra-lab replicates) and other strains. Data were processed to determine (gain or loss of) gene copy numbers. Strains could easily be distiguished based on gain/loss of prophage-like and CRISPR/Cas genes. We found that the model strain has multiple copies of the plasmid carrying the gene coding for tetanus toxin as well as several other genes. Data were reproducible within and between laboratories. The limit of detection of our method is an order of magnitude better than that of the pulsed-field gel electrophoresis (PFGE) currently used during manufacturing. This approach may part of an approach to reduce animal testing during vaccine manufacturing.

2020-02-15 | GSE144242 | GEO

Transcription profiling of Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) isolates

Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We have completed the full DNA sequence of one DT104 strain, NCTC13348 and show that the main differences between the genome of this isolate and the previously sequenced S. Typhimurium LT2 lie in integrated prophage elements and the Salmonella Genomic Island 1 encoding antibiotic resistance genes. Thirteen isolates of S. Typhimurium DT104 with different pulsed field gel electrophoresis (PFGE) profiles were analyzed by multi locus sequence typing (MLST), plasmid profiling, hybridization to a Pan-Salmonella DNA microarray and prophage-based multiplex PCR. All the isolates belonged to a single MLST type ST19. Microarray data demonstrated that the 13 DT104 isolates were remarkably conserved in gene content. The PFGE band-size differences in these isolates could be explained to a great extent by changes in prophage and plasmid content. Thus, here the nature of variation in different S. Typhimurium DT104 isolates is further defined at the genome level illustrating how this phage type is evolving over time.

2008-09-05 | E-MTAB-20 | biostudies-arrayexpress

Clostridium sp. DL-VIII

Project description:Clostridium sp. DL-VIII genome sequencing

| PRJNA42093 | ENA

Differences in the genomic content of Bordetella pertussis strains before and after vaccine introduction in European countries

Project description:Resurgence of pertussis has been observed in many countries with high vaccination coverage and clonal expansion of certain Bordetella pertussis strains has been associated with recent epidemics in Europe. It is known that vaccinations have selected strains which are different from those used for vaccine production. However, little is known about the differences in genomic content of strains circulating before the vaccination was introduced. In this study, we compared the genomes of 39 vaccine strains and old clinical isolates collected from Finland (N=5), Poland (N=14), Serbia (N=10) and the UK (N=10). The analysis included genotyping, pulsed-field gel electrophoresis (PFGE) and comparative genomic hybridisation (CGH). Compared to the strain Tohama I, the European strains analyzed have lost three major regions of difference (RD3, 5 and 29). However, difference in frequency of the absent RDs 3, 5 or 29 was observed among the four countries. Of the strains with absent RD5, half had also a duplicated region in the genome. All four RDs (RD22, 23, 24 and 26) absent in Tohama I were present in majority of the tested strains. Results obtained from PFGE analysis correlated well with those of CGH. Recently a novel pertussis toxin promoter allele (ptxP3) was described. Strains with ptxP3 have replaced resident ptxP1 strains. When the recent strains (N=22) selected from the four countries were examined, the ptxP3 allele was found in all countries except Poland. Our result indicates that at least three clusters of B. pertussis circulated in Europe in pre-vaccine era and their genomes were distinct from that of the reference strain Tohama I. Although progressive gene loss occurs in B. pertussis population with time, difference in frequency of the lost genes were observed among the countries. The observed differences in genomic content might be vaccine-driven.

2011-10-04 | GSE29579 | GEO

Recombinant and plasma-derived Factor VIII products induce distinct splenic cytokine microenvironments in hemophilia A

Project description:To investigate the gene expression in dendritic cells after treating hemiphilic mice with HBSS, plasma derived or recombinant factor VIII Gene expression in dendritic cells were measured 24 hours post treatment

2009-04-30 | GSE15809 | GEO

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