Comparative genomic hybridization of CHO Chr6 cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens Cricetulus griseus
PROVIDER: GSE56334 | GEO | 2014/06/05
SECONDARY ACCESSION(S): PRJNA242937
REPOSITORIES: GEO
Similar Datasets
Project description:Aim is to validate content of human genomic material in CHO cells monosomal for human chromosome 6. Comparative genomic hybridization to define human genomic regions maintained in hamster hybridoma cell line.
2014-06-05 | E-GEOD-56334 | biostudies-arrayexpress
Project description:Aim of this study is to test if a reference channel of a different array can be used to make array CGH more sensitive, cost effective and less labor intensive. The BT474 breast cancer cell line was compared to a mix of normal reference DNAs hybridized on different arrays and days and DNA copy number profiles were evaluated. Quality was assessed, using regular dual channel array CGH as a standard, using four quality measures; i.e. the MAD (median absolute deviation) value of chromosome 2, an amplitude of the ErbB2 gene amplification, a deletion on chromosome 9 and a deflection on chromosome 8. In addition, the use of a reference channel of a different array was tested for genomic DNA derived from formalin-fixed paraffin-embedded tumor tissue samples. This so called across array CGH (aaCGH) analysis yielded slightly higher quality chromosomal copy number profiles when using the same dye compared to analysis using two different dyes, both when exchanging fluorescent signals of hybridizations performed on different arrays and on different days. This approach avoids redundant hybridizations of the same reference material in every experiment and allows hybridization of two test samples on one array. AaCGH analysis substantially reduces cost of consumables and labor while yielding at least equivalent quality as the dual channel procedure. Keywords: array CGH data, across array CGH analysis
2007-12-31 | GSE8628 | 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.
2005-09-02 | E-SMDB-1524 | biostudies-arrayexpress
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:CHO-K1 (wildtype) and CHO-K6 (stablely overexpressing human HER2) cells were terated with 10 ug/ml transtuzumab or pertuzumab and their combination for 24 h and then the whole gene expression was analyzed by cDNA array.
2018-08-29 | GSE110189 | GEO
Project description:Transcriptomic data from CHO-S cells were gathered from multiple time points during batch culture to provide information about gene presence/absence for generation of a CHO-S cell line specific model using the GIMME algorithm.
2016-11-23 | GSE77800 | GEO
Project description:The genomic DNAs of strains JPCM5 and 263 of L. infantum, strains LV39 and Friedlin of L. major and strains Parrot-TarII and S125 of L. tarentolae were used in comparative genomic hybridizations to reveal the intra-species and inter-species gene content, and to validate L. tarentolae Parrot-TarII genome sequencing results. Leishmania (Sauroleishmania) tarentolae was first isolated in the lizard Tarentola mauritanica. This species is not known to be pathogenic to humans but is often used as a model organism for molecular analyses or protein overproduction. The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved by high-throughput sequencing technologies. The L. tarentolae genome was first assembled de novo and then aligned against the reference L. major Friedlin genome to facilitate contig positioning and annotation, providing a 23-fold coverage of the genome. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described, and it provides an opportunity for comparison with the completed genomes of the pathogenic Leishmania species. A high synteny was observed in de novo assembled contigs between all sequenced Leishmania species. A number of limited chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic with L. major. Globally, over 90% of the L. tarentolae gene content was shared with the other Leishmania species. There were 250 L. major genes absent from L. tarentolae, and interestingly these missing genes were primarily expressed in the intracellular amastigote stage of the pathogenic parasites. This implies that L. tarentolae may have impaired ability to survive as an intracellular parasite. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the leishmanolysin (GP63) and a gene related to the promastigote surface antigen (PSA31C). Overall, L. tarentolae appears to have a gene content more adapted to the insect stage rather than the mammalian one. This may partly explain its inability to replicate within mammalian macrophages and its suspected preferred life style as promastigote in the lizards.
2011-10-21 | GSE27184 | GEO
Project description:Transcriptional profiling of CHO-K1 cells comparing to in-house serum-free and suspension adapted CHO-K1 cells in the exponential phase. Goal was to determine the effects of serum on CHO-K1 cells.
2016-12-24 | GSE92885 | GEO
Project description:Haemophilus influenzae(Hi) is a gram-negative rod shaped bacterium that lives symbiotically in the upper respiratory tract of humans. Capsulated Hi, as well as non-capsulated strains are known to cause a number of significant infections. Recognizing and understanding the links between the phenotypic traits and the genetic background has paramount epidemiological and clinical importance. To date, a panoply of microbiological and molecular biology tools have been developed and utilized by researchers aimed at identifying the evolutionary links among strains and isolates. Comparative genomic hybridization (CGH) has been shown to be a useful tool for screening strains for their genetic content. However, there is a major limitation when CGH is conducted on a microarray based on a single reference genome. CGH results report which genes are present or absent relative to the genome. Hence the information about novel genetic content that the query strain possesses remains obscure. We report here the construction of the first Hi pan-genome microarray representing ca. 4600 features by 70-mers. In addition to those from the Rd strain, new features originate from the unfinished genome sequences present in NCBI database and from our novel gene discovery project efforts using strain HK1212. Genomes of 20strains belonging to different phylogenetic lineages were screened for their gene loss and gain utilizing the species microarray. The results obtained by employing the multistrain species microarray provide comprehensive information about the genomic content of uncharacterized strains. The trees generated by CGH, in general, do not reproduce the phylogeny of a species in terms of vertical evolution, but instead represents the overall relatedness of genomes to one another and provide an assessment about the species genome evolution. Keywords: Comparative Genomic Hybridization
2009-09-09 | GSE8300 | GEO