Ontology highlight
ABSTRACT:
PROVIDER: PRJNA835501 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19103575_1.fastq.gz | Fastqsanger.gz | |||
| SRR19103575_2.fastq.gz | Fastqsanger.gz | |||
| SRR19103576_1.fastq.gz | Fastqsanger.gz | |||
| SRR19103576_2.fastq.gz | Fastqsanger.gz | |||
| SRR19103577_1.fastq.gz | Fastqsanger.gz |
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Project description:DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads. DNA genome sequencing at roughly 0.03 coverage to identify genomic copy number variations
2010-04-02 | E-GEOD-21159 | biostudies-arrayexpress
Project description:DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.
2010-04-02 | GSE21159 | GEO
Project description:A major limitation to improving small-molecule pharmaceutical production in streptomycetes is the inability of high-copy-number plasmids to tolerate large biosynthetic gene cluster inserts. A recent finding has overcome this barrier. In 2003, Hu et al. discovered a stable, high-copy-number, 81-kb plasmid that significantly elevated production of the polyketide precursor to the antibiotic erythromycin in a heterologous Streptomyces host (J. Ind. Microbiol. Biotechnol. 30:516-522, 2003). Here, we have identified mechanisms by which this SCP2*-derived plasmid achieves increased levels of metabolite production and examined how the 45-bp deletion mutation in the plasmid replication origin increased plasmid copy number. A plasmid intramycelial transfer gene, spd, and a partition gene, parAB, enhance metabolite production by increasing the stable inheritance of large plasmids containing biosynthetic genes. Additionally, high product titers required both activator (actII-ORF4) and biosynthetic genes (eryA) at high copy numbers. DNA gel shift experiments revealed that the 45-bp deletion abolished replication protein (RepI) binding to a plasmid site which, in part, supports an iteron model for plasmid replication and copy number control. Using the new information, we constructed a large high-copy-number plasmid capable of overproducing the polyketide 6-deoxyerythronolide B. However, this plasmid was unstable over multiple culture generations, suggesting that other SCP2* genes may be required for long-term, stable plasmid inheritance.
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Project description:Increased Plasmid Copy-number is Essential for Yersinia T3SS Function and Virulence
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Project description:Increased copy number couples the evolution of plasmid horizontal transmission and antibiotic resistance.
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Project description:Genomic copy number variation induced by TAQing system in Saccharomyces cerevisiae.
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Project description:Genomic copy number variation induced by TAQing system in Arabidopsis thaliana.
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Project description:The Streptomyces coelicolor two genes operon SCO5784-SCO5785 encodes a two-component system which functions in a similar manner to that of the Bacillus subtilis DegS-DegU system. Propagation of the regulatory gene in high copy number results in the overproduction of several extracellular enzymes, among them the major extracellular protease, as well as in a higher level of synthesis of the antibiotic actinorhodin. This two-component system seems to control various processes characterised by the transition from primary to secondary metabolism in S. coelicolor, as determined by proteomic and transcriptomic analices. The presence of the regulatory gene in high copy number in S. coelicolor additionally seems to elicit a stringent response in the bacterial cell. Therefore, we propose renaming S. coelicolor genes SCO5784 and SCO5785 as degS and degU, respectively. All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. Hybridisation assays were carried out with cDNA obtained from RNA extracted at the late exponential phase of growth (24h). The transcriptional profile of wild type (S. coelicolor M145) cells carrying the multicopy plasmid pIJ487 was compared with that of the same strain carrying the degU gene cloned in the same plasmid under the control of its own promoter (S. coelicolor M28). And the transcriptional profile of wild type (S, coelicolor M145) cells was compared to that of the DegU deficient strain (S. coelicolor I32).
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