Mouse Cells Time of Replication (ToR)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE17229 | GEO | 2010/05/25
SECONDARY ACCESSION(S): PRJNA123665
REPOSITORIES: GEO
Similar Datasets
Project description:Measurment of the ToR by comapring the DNA content of the S phase and the DNA content of the G1 phase, the method is based on the method used in the paper - Replication timing of the human genome by Woodfine et al. that was published in Hum. Mol. Genet. 2004. Briefly, after staining with Propidium Iodide, cells in G1 and S phase of the cell cycle are sorted by FACS sorter (ARIA or Vantage), DNA is then extracted from the fractions and differentially labeled with dUTP-Cy3 or dUTP-Cy5 using direct labeling (Agilent labeling kit). The labeled DNA is cohybridized to the array. Early replicating sequences correspond to the spots with high S/G1 ratio and late replicating sequences correspond to the spots with low S/G1 ratio.
2010-05-25 | GSE17235 | GEO
Project description:Measurment of the ToR by comapring the DNA content of the S phase and the DNA content of the G1 phase, the method is based on the method used in the paper - Replication timing of the human genome by Woodfine et al. that was published in Hum. Mol. Genet. 2004. Briefly, after staining with Propidium Iodide, cells in G1 and S phase of the cell cycle are sorted by FACS sorter (ARIA or Vantage), DNA is then extracted from the fractions and differentially labeled with dUTP-Cy3 or dUTP-Cy5 using direct labeling (Agilent labeling kit). The labeled DNA is cohybridized to the array. Early replicating sequences correspond to the spots with high S/G1 ratio and late replicating sequences correspond to the spots with low S/G1 ratio. two mouse tissues were measured (MEF and L1210), 2 replicates for each sample
2010-05-25 | E-GEOD-17229 | biostudies-arrayexpress
Project description:Measurment of the ToR by comapring the DNA content of the S phase and the DNA content of the G1 phase, the method is based on the method used in the paper - Replication timing of the human genome by Woodfine et al. that was published in Hum. Mol. Genet. 2004. Briefly, after staining with Propidium Iodide, cells in G1 and S phase of the cell cycle are sorted by FACS sorter (ARIA or Vantage), DNA is then extracted from the fractions and differentially labeled with dUTP-Cy3 or dUTP-Cy5 using direct labeling (Agilent labeling kit). The labeled DNA is cohybridized to the array. Early replicating sequences correspond to the spots with high S/G1 ratio and late replicating sequences correspond to the spots with low S/G1 ratio. two human tissues were measured (MOLT4 and FFT-foreskin fibroblasts), 2 replicates for each sample
2010-05-24 | E-GEOD-17235 | biostudies-arrayexpress
Project description:To investigate the transcriptional profile of GVE2 genes, the viral genes were identified by DNA microarray with Cy5- or Cy3-dUTP-labeled cDNAs prepared from uninfected and GVE2-infected Geobacillus sp. E263 at 4 h p.i.. After hybridization with the Cy3-dUTP-labeled cDNAs from GVE2-infected Geobacillus sp. E263 at 4 h p.i., Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263 as well as Cy3- dUTP-labeled yeast cDNAs and Hex DNA, many spots produced positive signals significantly above the background, while no signal appeared for the Cy5-dUTP-labeled cDNAs from uninfected Geobacillus sp. E263., indicating that the positive signals represented the GVE2 gene transcripts detectable by DNA microarray. The DNA fragments, detected to be positive in the reverse transcripts at 4 h p.i., contained 74.2% of the presumptive GVE2 ORFs. Keywords: Transcriptional profile of thermophilic bacteriophage at 4 h p.i.
2006-08-26 | GSE5577 | GEO
Project description:Antimetabolite chemotherapies increase uracil levels in DNA, and thus identification of factors that influence the uracil content in DNA may have implications for understanding uracil-mediated chromosomal instability. We previously showed in the budding yeast Saccharomyces cerevisiae that uracil content in DNA correlates with replication timing, where the earliest and latest replicating regions are depleted in uracil. Here, we manipulated nucleotide biosynthesis enzymes in budding yeast to determine whether the pattern of uracil incorporation could be altered. In strains with high levels of uracil incorporation, deletion of dCMP deaminase (Dcd1) accelerated uracil incorporation at early-firing origins, likely due to rapid dTTP pool depletion. In contrast, increasing the activity of ribonucleotide reductase, which is required for the synthesis of all dNTPs via ribonucleotide diphosphates, lead to dUTP and dTTP pool equilibration and a concomitant increase in uracil content throughout the genome. These data suggest that uracil availability and the dUTP:dTTP ratio are temporally regulated during S phase and govern uracil incorporation into the genome. Therapeutic manipulation of nucleotide biosynthesis in human cells to either increase the dUTP pool or deplete the dTTP pool in early S phase may therefore improve the efficacy of antimetabolite chemotherapies.
2016-09-23 | GSE73364 | GEO
Project description:The changes in global gene expression in response to DNA damage may derive from either direct induction or repression by transcriptional regulation or indirectly by synchronization of cells to specific cell cycle phases, such as G1 or G2. We developed a model that successfully estimated the expression levels of >400 cell-cycle-regulated genes in normal human fibroblasts based on the proportions of cells in each phase of the cell cycle. By isolating effects on the gene expression associated with the cell cycle phase redistribution after genotoxin treatment, the direct transcriptional target genes were distinguished from genes for which expression changed secondary to cell synchronization. Application of this model to ionizing radiation (IR)-treated normal human fibroblasts identified 150 of 406 cycle-regulated genes as putative direct transcriptional targets of IR-induced DNA damage. Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization. Experiment Overall Design: Normal human fibroblasts were synchronized and harvested at G0, G1, S G2 and M cell cycle phase, and logarithmically growing cells were treated with 1.5 Gy IR or sham, and harvested at 2, 6 or 24 h after the treatment. Total RNA was isolated using Qiagen RNeasy kit. The quality of all RNA samples was confirmed using an Agilent 2100 Bioanalyzer. Microarray analysis was then performed: briefly, 1 µg of sample RNA and global reference RNA (Stratagene) were converted to cDNA with reverse transcriptase then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP (Agilentâ??s Low RNA Input Linear Amplification Kit). The quality of each labeled cRNA was evaluated using an Agilent 2100 Bioanalyzer prior to hybridization. 750ng of Cy3 and Cy5-labeled cRNA were used in the hybridization. The labeled cRNA from sham- or IR-treated samples was hybridized with the labeled global reference cRNA on an Agilent 22k human 1A array in a hybridization oven (Robbins Scientific Model 400, 1040-60-1AG) at 60oC for 17 h. Hybridization of sample RNA against reference RNA was done twice with dye swap. Following hybridization, the arrays were scanned using the Agilent DNA Microarray Scanner with SureScan® Technology and microarray images were analyzed using Agilent Feature Extraction Software (v7.1). The gene expression level was presented as ratio of sample intensity against reference intensity.
2008-06-15 | E-GEOD-7075 | biostudies-arrayexpress
Project description:DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins RPA, SMC5, gamma-H2AX, and BRCA1 in B cells subjected to replication stress.
2013-02-04 | GSE43504 | GEO
Project description:Replication timing in Saccharomyces cerevisiae in various replication stress conditions using CGH microarrays of S vs G1 cells. Replication of the eukaryotic genomes follows a characteristic temporal program, with different regions replicating at different times in S phase. We describe a stochastic model of DNA replication that naturally explains the replication profiles of a dozen of S. cerevisiae mutants. Each profile is described by a single parameter that differ between the mutants: the ratio between the fork velocity and the typical initiation rate (the “replicon length”), while all other origin-specific parameters remain unchanged. We devise an analytical method to infer the replicon lengths from the available data, and predicted its value in different mutant backgrounds. Further experiments verified model’s predictions. Our study supports a stochastic model of DNA replication in S. cerevisiae and explains the apparent robustness of this profile to perturbations that extend S phase. DNA from FACS-sorted cells was extracted, labeled with Cy dyes, hybridized to the CGH microarray and scanned. 18 strains were used, with variable biological repeats number.
2011-09-08 | E-GEOD-32002 | biostudies-arrayexpress
Project description:DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins DNA double strand breaks (DSBs) in B lymphocytes are thought to arise stochastically during replication (S phase) or as a result of targeted DNA damage by activation induced cytidine deaminase (AID) in G1. Here we identify a novel class of recurrent, early replicating and AID independent DNA lesions, termed early replication fragile sites (ERFS), by genome-wide localization of DNA repair proteins RPA, SMC5, gamma-H2AX, and BRCA1 in B cells subjected to replication stress. Protein-DNA association for four DNA damage response proteins (RPA, SMC5, g-H2AX, BRCA1), BrdU incorporation, and gene transcription in B lymphocytes with and without hydroxyurea treatment were examined.
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