Ontology highlight
ABSTRACT:
PROVIDER: PRJNA714684 | ENA |
REPOSITORIES: ENA
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Project description:Using a human-hamster radiation hybrid panel (G3), we have mapped loci regulating gene expression due to copy number increase. Copy number from radiation hybrid clones were measured relative to the A23 hamster recipient line. Expression from 79 radiation hybrid clones were measured in duplicate and compared to expression of the A23 hamster recipient line (GA_illumina_expression1 and GA_illumina_expression2). Expression of liver, kidney and heart from human and hamster are also included (GA_illumina_expression_R).
2012-04-08 | E-GEOD-19003 | biostudies-arrayexpress
Project description:Using a chicken-hamster radiation hybrid panel (ChickRH6), we have mapped chicken chromosome(s) that contain possible factor(s) that permit avian polymerase activity, by increasing polymerase activity. We identified four hybrid clones permissive for polymerase activity. Activity was lost following 12 passages respectively in only one of the positive clones. Expression from the four positive radiation hybrid clones at passages 1, and 12 was measured and compared to expression of the hamster recipient line and 17 negative (for polymerase activity) clones.
2015-12-01 | E-MTAB-3643 | biostudies-arrayexpress
Project description:Using a human-hamster radiation hybrid panel (G3), we have mapped loci regulating gene expression due to copy number increase.
2012-04-09 | GSE19003 | GEO
Project description:To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for differences in radiation sensitivity, all experiments were performed with two different embryonic fibroblast strains. After a single dose of 2 Gray more than half of the irradiated clones exhibited radiation-induced genomic instability (RIGI). Methylation arrays identified several hundred differentially methylated genes and nine enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis.
2018-04-10 | GSE112873 | GEO
Project description:To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for differences in radiation sensitivity, all experiments were performed with two different embryonic fibroblast strains. After a single dose of 2 Gray more than half of the irradiated clones exhibited radiation-induced genomic instability (RIGI). Methylation arrays identified several hundred differentially methylated genes and nine enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis.
2018-04-07 | GSE112812 | GEO
Project description:PBRM1 deficiency in immortalised fibroblast cell line 1BR3-hTERT after ionising radiation treatment leads to more mitotic progression and more formation of micronucleated cells. Here, we performed total RNA-seq in 1BR3-hTERT parental line and PBRM1 knockout clones (PBRM1 KO3&KO5) under untreated (UT) or 48 hr post 6Gy irradiation condition. We found that the annotated DREAM complex target genes are less transcriptionally repressed in the 1BR3-hTERT PBRM1 knockout clones compared to the parental line after ionising radiation treatment. The results confirm our findings that PBRM1 deficiency leads to delayed p21 induction and delayed p130 hypo-phosphorylation, which leads to defective DREAM target gene repression and misregulated G2/M progression after ionising radiation treatment.
2022-09-07 | GSE183688 | GEO
Project description:CGH arrays for Smukowski Heil, et al MBE 2017. Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we address these questions using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae x Saccharomyces uvarum and their parentals. We evolved these strains in nutrient limited conditions for hundreds of generations and sequenced the resulting cultures to identify genomic changes. Analysis of 16 hybrid clones and 16 parental clones identified numerous point mutations, copy number changes, and loss of heterozygosity events, including species biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated loss of heterozygosity at the high affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the loss of heterozygosity is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity, and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
2017-02-21 | GSE95086 | GEO
Project description:Intra-tumor heterogeneity is a hallmark of glioblastoma multiforme, and thought to negatively affect treatment efficacy. Here we establish libraries of glioma-initiating cell (GIC) clones from patient samples and find extensive molecular and phenotypic variability between clones, including a wide range of responses to radiation and drugs. This widespread variability was observed as a continuum of multitherapy resistance phenotypes linked to a proneural-to-mesenchymal shift in the transcriptome.
2016-12-13 | GSE89398 | GEO
Project description:An irradiated but chromosomally stable CHO clone RT210B was used a reference to find differences in gene expression compared to radiation-induced chromosomally unstable isogenic clones. Equal quantities of two unstable different unstable clones were mixed prior to RNA extraction. Each mixture was tested twice versus the stable reference clone. Two different two clone mixtures were tested against the same chromosomally stable clone Keywords: repeat sample
2004-08-01 | GSE1626 | GEO