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Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

ABSTRACT: Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

PROVIDER: PRJNA793235 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17382834_1.fastq.gz	Fastqsanger.gz
	SRR17382834_2.fastq.gz	Fastqsanger.gz
	SRR17382835_1.fastq.gz	Fastqsanger.gz
	SRR17382835_2.fastq.gz	Fastqsanger.gz
	SRR17382836_1.fastq.gz	Fastqsanger.gz

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Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

Project description:we designed a CRISPR-based chromosome-doubling technique to construct an artificial diploid Escherichia coli cell. The stable diploid E. coli was confirmed by quantitative PCR and third-generation genome sequencing.

2022-12-29 | GSE192799 | GEO

Artificial Diploid Escherichia coli by a CRISPR Chromosome-Doubling Technique.

Project description:Synthetic biology has been represented by the creation of artificial life forms at the genomic scale. In this work, a CRISPR-based chromosome-doubling technique is designed to first construct an artificial diploid Escherichia coli cell. The stable single-cell diploid E. coli is isolated by both maximal dilution plating and flow cytometry, and confirmed with quantitative PCR, fluorescent in situ hybridization, and third-generation genome sequencing. The diploid E. coli has a greatly reduced growth rate and elongated cells at 4-5 µm. It is robust against radiation, and the survival rate after exposure to UV increased 40-fold relative to WT. As a novel life form, the artificial diploid E. coli is an ideal substrate for research fundamental questions in life science concerning polyploidy. And this technique may be applied to other bacteria.

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Project description:Construction of an artificial diploid Escherichia coli using a CRISPR-based chromosome-doubling technique

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Genetic map construction of a diploid blueberry mapping population

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RNA-seq comparison: before/after MARIS protocol and library construction technique test

Project description:The aim of this experiment was to determine the amount of RNA-seq signal degradation that results from MARIS and to test how well 4 different RNA-seq library construction techniques perform on partially degraded RNA.

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Diploid oat

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Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

Project description:Here we report the design, construction and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ~190 kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporated orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up new opportunities to directly test hypotheses surrounding these essential non-coding RNAs

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Gene expression profile of diploid and tetraploid mouse primary hepatocyte

Project description:Genetically unstable tetraploid cells can promote tumorigenesis. Recent estimates suggest that ~37% of human tumors have undergone a genome-doubling event during their development. This potentially oncogenic effect of tetraploidy is countered by a p53-dependent barrier to proliferation. However, the cellular defects and corresponding signaling pathways that trigger growth suppression in tetraploid cells are not known. Here we combine genome-scale RNAi screening and in vitro evolution approaches to demonstrate that cytokinesis failure activates the Hippo tumor suppressor pathway in cultured cells as well as in naturally occurring tetraploid cells in vivo. Induction of the Hippo pathway is triggered in part by extra centrosomes, which alter small G-protein signaling and activate LATS2 kinase; LATS2 in turn stabilizes p53 and inhibits the transcriptional regulators YAP and TAZ. These findings define an important tumor suppression mechanism. Furthermore, our experiments uncover adaptations that allow nascent tumor cells to bypass this inhibitory regulation. Hepatocytes of newborn mice are initially diploid, but become progressively tetraploid with age. To study the mechanism of cell cycle arrest in naturally occurred tetraploidy, we used microarrays to detail the overall gene expression profile of diploid and tetraploid primary hepatocytes and identified YAP target genes up-regulated in diploid cells.

2017-02-10 | GSE57769 | GEO

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