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Gene regulation in ES cell lines with different nuclei donor cell sources

ABSTRACT: Comparison of ES cell line of different genetic background and different cloning methods to identify changes on gene expression levels between these ES cell lines. The main question behind the experiments id, if there is major/important difference on gene expression level between NT embryo-derived ES cell liens and control embryo derived ES cell lines. Ih has an effect on therapeutic cloning that means the nuclei donor cell source could be an important question. We also included different genetic background cell lines (HM-1 is 129/SV, #4 ES cell line is B6D2F1 derived heterozygote cell line) to compare the effect of gentic background differences. Hetero- and homozygosis con be compared based on the PGA ES cell line from the same genetic backgound. Keywords: cDNA microarray, murine ES cells, nucleous transfer

ORGANISM(S): Mus musculus

PROVIDER: GSE8424 | GEO | 2008/05/30

SECONDARY ACCESSION(S): PRJNA101479

REPOSITORIES: GEO

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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. 9 custom 2.1M high density aCGH were performed to test the genome integrity in 3 independent bovine transgenic cell lineages generated from serial rounds of genetic modification and cloning, accommodating the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines that are drastically different in cloning efficiency.