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ABSTRACT: Avirulence gene cloning using RADseq markers

PROVIDER: PRJNA335917 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR3990580_1.fastq.gz	Fastqsanger.gz
	SRR3990580_2.fastq.gz	Fastqsanger.gz
	SRR3990590_1.fastq.gz	Fastqsanger.gz
	SRR3990590_2.fastq.gz	Fastqsanger.gz
	SRR3990600_1.fastq.gz	Fastqsanger.gz

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Assessment of genome integrity with array CGH of cattle transgenic cell lines produced by homologous recombination and somatic cell cloning

Project description:Background Transgenic cattle carrying multiple genomic modifications have been produced by sequential gene targeting and serial rounds of somatic cell chromatin transfer (cloning). However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity, rendering a decline in cloning. To test this possibility, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning. Our plan included the control hybridizations (self to self) of 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency. Results We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cloning efficiency cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). Conclusions Our findings reveal that large copy number genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline.

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