Bos taurus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA135377 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2011-05-23 | E-GEOD-26132 | biostudies-arrayexpress
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.
2011-05-23 | GSE26132 | GEO
Project description:HS-10502 is a Poly(ADP-ribose) polymerase 1 (PARP1)-specific selective inhibitor. The purpose if this study is to assess the safety, tolerability, pharmacokinetics (PK), and efficacy of HS-10502 in subjects with homologous recombination repair (HRR) gene mutant or homologous recombination deficiency (HRD) positive advanced solid tumors.
| 9330 | ecrin-mdr-crc
Project description:Somatic non-allelic homologous recombination caused by repeat elements
| PRJNA636606 | ENA
Project description:Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map- based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology.
2005-09-02 | E-SMDB-1524 | biostudies-arrayexpress
Project description:Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map- based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-09-09 | GSE3269 | GEO
Project description:Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map- based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Using regression correlation
2005-09-09 | E-GEOD-3269 | biostudies-arrayexpress
Project description:Homologous recombination (HR) is an essential and highly regulated cellular process. Unintended HR in somatic cells is potentially deleterious; it can result in translocations and/or somatic cell loss of heterozygosity. This is suppressed by the BLM protein in combination with topoisomerase III, RMI1 and RMI2 in a hetero-tetrameric complex (the ‘Bloom’s complex’). To understand how the activities of BLM helicase and topoisomerase III are coupled, we purified the four-subunit complex. Chemical crosslinking and mass spectrometry revealed a unique architecture that couples helicase and topoisomerase domains.
2022-01-17 | PXD011078 | Pride
Project description:A Phase 2, open-label, single-arm trial to evaluate the response of rucaparib in participants with various solid tumors and with deleterious mutations in Homologous Recombination Repair (HRR) genes.
| 2322588 | ecrin-mdr-crc
Project description:Recent success in the derivation of mouse haploid embryonic stem cells from androgenetic blastocysts (ahESCs) has provided new avenues for the generation of genetically modified animals. However, the efficiency to produce viable transgenic mice via intracytoplasmic ahESCs injection (ICAI) was very low, which may correlate with the aberrant regulation of imprinted genes. Here we designed to delete the paternal imprinted gene H19 by CRSPR-Cas9 system combined with homologous recombination. The H19 deleted (H19Î) ahESCs maintained haploidy and genome integrity, expressed pluripotency markers, differentiated into embryoid bodies (EBs), and contributed to chimeras after blastocyst injection. These cells exhibited similar imprinting features with sperm cells, and can produce fertile progenies after ICAI at a high efficiency. More importantly, it is feasible to perform genetic manipulations in H19Î ahESCs, and the genomic modifications can be properly transmitted to offspring. Our study will benefit the reproductive medicine in curing the hereditary genetic diseases and infertility in the future. The copy number variations of the two H19Î ahESC lines were analyzed by the SurePrint G3 Mouse CGH 4Ã180 K microarrays (Agilent). Wild-type OG-3 ahESCs were used as reference.
2015-11-05 | E-GEOD-67563 | biostudies-arrayexpress