Streptococcus pneumoniae CGSP14
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ABSTRACT:
PROVIDER: PRJNA29179 | ENA |
REPOSITORIES: ENA
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Project description:PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance.
2011-08-01 | GSE29501 | GEO
Project description:Strain for comparative analysis
| PRJNA32767 | ENA
Project description:Strain for comparative analysis
| PRJNA32279 | ENA
Project description:Comparative genome analysis of S. pneumoniae clinical isolates
| PRJNA89131 | ENA
Project description:Comparative genome analysis of S. pneumoniae clinical isolates
| PRJNA89129 | ENA
Project description:Comparative genome analysis of S. pneumoniae clinical isolates
| PRJNA89135 | ENA
Project description:Comparative genome analysis of S. pneumoniae clinical isolates
| PRJNA89133 | ENA
Project description:PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. The Pneumococcus are among most deadly pathogens world-wide. The infections and outbreaks caused by this pathogens is quite frequent despite existing diagnostic network and therapeutic means. Therefore, developing reliable diagnostic tools and efficient (broad-spectrum) therapeutics for Streptococcus pneumoniae remain a public health priority for every country in world today. The comparative genomics study will provide the largest hitherto genomic data sets regarding this pathogen.These large data sets will enable us as well as other members of scientific community to conduct comprehensive data mining in the form of gene association studies with statistical power and significance. Two hundread fifty five query strains were investigated in this study, with each query strain hybridized against the reference strain, tigr4. Each strain has a single dye experiment. Each oligo is spotted on the S.pneumoniae species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome of S. pneumoniae and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.
2011-07-31 | E-GEOD-29501 | biostudies-arrayexpress
Project description:We performed a comparative study of the two control sample options with a Streptococcus pneumoniae microarray designed with three fully sequenced strains. We hybridized two of these strains (R6 and G54) as test samples using the third strain alone (TIGR4) or a mix of the three strains as the control sample.
2008-04-30 | E-MEXP-1390 | biostudies-arrayexpress
Project description:The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Separate domains were identified depending of the transcription of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show here that these distinct domains have different expression and conservation tendencies. Microarray fluorescence units under non-relaxation conditions, taken as a measure of gene transcription level, were significantly lower in F genes than in the other domains in the same range of AT content. Transcription level categorization of the domains was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences evidenced conservation of gene composition in the U and D domains and extensive gene interchange in F domains. We tested domain organization by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology works as a general transcriptional regulator, superimposed to other kind of more specific regulatory mechanisms.
2014-12-29 | GSE58186 | GEO