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Links from GEO DataSets

Items: 20

1.

S-phase time-course of Lachancea kluyveri cells

(Submitter supplied) Haploid cells of Lachancea kluyveri were arrested in G1 phase using Saccharomices cerevisiae alpha factor. After, release in a new media, cells go synchronously through S-phase. One sample is taken every five minutes. Microarrays are used to monitor the change of DNA copy number from 1 to 2, all along the genome during S-phase.
Organism:
Lachancea kluyveri
Type:
Genome variation profiling by genome tiling array
Platform:
GPL15421
24 Samples
Download data: GPR
Series
Accession:
GSE37244
ID:
200037244
2.

ssDNA in S phase compared to G1 phase at different timepoints

(Submitter supplied) To identify origins of replication in Lachancea waltii by mapping regions of ssDNA that are enriched in S phase.
Organism:
Lachancea waltii
Type:
Other
Platform:
GPL15109
6 Samples
Download data: TXT
Series
Accession:
GSE35253
ID:
200035253
3.

Density Transfer Data for Lachancea waltii DNA Replication Profile

(Submitter supplied) Array data detailing the progression of DNA replication in the yeast Lachancea waltii.
Organism:
Lachancea waltii
Type:
Other
Platform:
GPL15109
8 Samples
Download data: TXT
Series
Accession:
GSE35155
ID:
200035155
4.

Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL14887 GPL13821
34 Samples
Download data: PAIR
Series
Accession:
GSE55156
ID:
200055156
5.

Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome [ChIP-Seq]

(Submitter supplied) Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL13821
4 Samples
Download data: TXT
6.

Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome [array]

(Submitter supplied) Chromosomal DNA replication involves the coordinated activity of hundreds to thousands of replication origins. Individual replication origins are subject to epigenetic regulation of their activity during S-phase, resulting in differential efficiencies and timings of replication initiation during S-phase. This regulation is thought to involve chromatin structure and organization into timing domains with differential ability to recruit limiting replication factors. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL14887
30 Samples
Download data: PAIR
Series
Accession:
GSE55130
ID:
200055130
7.

ORC binding profile in Candida albicans

(Submitter supplied) Map ORC binding sites to identify replication origins in C. albicans by using polyclonal ORC antibodies (gift from Stephen Bell Lab). Due to the unsynchronized nature of Candida cells, log-phase cultures were taken to perfoem ChIP-chip experiments to find the genome-wide ORC binding sites.
Organism:
Candida albicans
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL18278
7 Samples
Download data: TXT
Series
Accession:
GSE54923
ID:
200054923
8.

Separation of DNA replication from the assembly of break-competent meiotic chromosomes

(Submitter supplied) The meiotic cell division reduces the chromosome number from diploid to haploid to form gametes for sexual reproduction. Although much progress has been made in understanding meiotic recombination and the two meiotic divisions, the processes leading up to recombination, including the prolonged pre-meiotic S phase (meiS) and the assembly of meiotic chromosome axes, remain poorly defined. We have used genome-wide approaches in Saccharomyces cerevisiae to measure the kinetics of pre-meiotic DNA replication, and to investigate the interdependencies between replication and axis formation. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array; Genome variation profiling by genome tiling array; Other
Platforms:
GPL3499 GPL5991
54 Samples
Download data: TXT
Series
Accession:
GSE35667
ID:
200035667
9.

DSB formation in replication compromised cells

(Submitter supplied) DSBs were mapped genome-wide by ssDNA enrichment in cdc6-mn replication comprimsied strains.
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL5991
2 Samples
Download data: TXT
Series
Accession:
GSE35666
ID:
200035666
10.

S phase and HU profiles in wild-type and mutant cells

(Submitter supplied) Total S phase was measured for wild-type cells undergoing meiS and mitS. Early replication origins were mapped in mitS in wild-type cells, and in meiS for wild-type, sml1 delete, rec8 delete and spo11 delete cells.
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by genome tiling array
Platforms:
GPL3499 GPL5991
24 Samples
Download data: TXT
Series
Accession:
GSE35662
ID:
200035662
11.

Chromatin IP for Mcm2-7, Rec8, Hop1 and Red1

(Submitter supplied) Mcm2-7 ChIP in pre-meiotic and pre-mitotic cells, axis factor ChIP in wild-type and replication compromised strains in meiosis
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL5991 GPL3499
28 Samples
Download data: TXT
Series
Accession:
GSE35658
ID:
200035658
12.

Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase

(Submitter supplied) In order to address the replication timing of the centromeres in yeast Candida albicans, we have determined at high temporal and spatial resolution its genome-wide DNA replication timing profile. This was done by sorting S- and G1-phase cells by FACS and hybridizing DNA from both fractions onto genomic tiling arrays. Data was normalized, organized by chromosomal positition, and smoothed. Replication timing is inferred from the DNA copy number along the chromosome with data peaks corresponding to predicted origins of DNA replication. more...
Organism:
Candida albicans
Type:
Other
Platforms:
GPL9148 GPL9150
6 Samples
Download data: SRR, TXT
Series
Accession:
GSE17963
ID:
200017963
13.

Genome-wide mapping of DNA re-replication in S. cerevisiae

(Submitter supplied) To maintain genomic stability, re-initiation of eukaryotic DNA replication within a single cell cycle is blocked by multiple mechanisms that inactivate or remove replication proteins after G1 phase. Consistent with the prevailing notion that these mechanisms are redundant, we previously showed that simultaneous deregulation of three replication proteins, ORC, Cdc6 and Mcm2-7, was necessary to cause detectable bulk re-replication in G2/M phase in Saccharomyces cerevisiae. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by genome tiling array
Platform:
GPL3412
50 Samples
Download data
Series
Accession:
GSE4181
ID:
200004181
14.

Conservation of replication timing reveals global and local regulation of replication origin activity.

(Submitter supplied) DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. more...
Organism:
Saccharomyces cerevisiae; Saccharomyces bayanus; Saccharomyces arboricola; Saccharomyces paradoxus; Saccharomyces bayanus x Saccharomyces cerevisiae
Type:
Genome variation profiling by high throughput sequencing
5 related Platforms
10 Samples
Download data: FA, TXT, WIG
Series
Accession:
GSE36045
ID:
200036045
15.

Single stranded DNA formation during S phase in the presence of hydroxyurea in S. cerevisiae and S. pombe

(Submitter supplied) We have developed a method to analyze single-stranded DNA (ssDNA) formation on a genomic scale by using microarrays. Using this technique we have assessed the location and the amount of ssDNA in S. cerevisiae during DNA replication. We have observed that when replication is impeded by hydroxyurea, ssDNA formation can be detected in both wild type and the checkpoint-deficient rad53 cells. However, while wild type cells showed ssDNA formation at only a subset of origins, rad53 cells formed ssDNA at virtually all known origins. more...
Organism:
Schizosaccharomyces pombe; Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL3388 GPL3398
10 Samples
Download data
Series
Accession:
GSE4099
ID:
200004099
16.

Regulatory Mechanisms That Prevent Re-initiation of DNA Replication Can Be Locally Modulated at Origins by Nearby Sequence Elements

(Submitter supplied) Eukaryotic cells must inhibit re-initiation of DNA replication at each of the thousands of origins in their genome because re-initiation can generate genomic alterations with extraordinary frequency. To minimize the probability of re-initiation from so many origins, cells use a battery of regulatory mechanisms that reduce the activity of replication initiation proteins. Given the global nature of these mechanisms, it has been presumed that all origins are inhibited identically. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by genome tiling array
Platform:
GPL3412
282 Samples
Download data: GPR
Series
Accession:
GSE55420
ID:
200055420
17.

Genome-wide localization of ORC and MCM binding sites and identification of replication origins in S. pombe

(Submitter supplied) DNA replication of eukaryotic chromosomes initiates at a number of discrete loci, called replication origins. Distribution and regulation of origins are important for complete duplication of the genome. Here, we determined locations of Orc1 and Mcm6, components of pre-replicative complex (pre-RC), on whole genome of Schizosaccharomyces pombe using a high-resolution tiling array. Pre-RC sites were identified in 460 intergenic regions, where Orc1 and Mcm6 colocalized. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL3847
10 Samples
Download data: CEL
Series
Accession:
GSE6523
ID:
200006523
18.

High-resolution genome replication profiles, modeling and single-cell imaging define the stochastic nature of replication initiation and termination

(Submitter supplied) Eukaryotic genome replication is stochastic with each cell using a different cohort of replication origins. Interpreting high-resolution genome replication profiles with a mathematical model allowed us to quantify the stochastic nature of genome replication. This approach included estimation of the activity of every replication origin and the genome-wide location of replication termination events. Single-cell measurements verified the inferred values for stochastic origin replication time. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL16234
16 Samples
Download data: WIG
19.

Genome-wide Analysis of Re-replication Reveals Inhibitory Controls that Target Multiple Stages of Replication Initiation

(Submitter supplied) DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome variation profiling by array; Genome variation profiling by genome tiling array
Platforms:
GPL3499 GPL884
24 Samples
Download data
Series
Accession:
GSE4487
ID:
200004487
20.

Rif1 is a global regulator of timing of replication origin firing in fission yeast

(Submitter supplied) One of the long-standing questions in eukaryotic DNA replication is the mechanisms that determine where and when a particular segment of the genome is replicated. Cdc7/Hsk1 is a conserved kinase required for initiation of DNA replication, and may affect the site selection and timing of origin firing. We identified rif1∆, a null mutant of rif1+, a conserved telomere binding factor, as an efficient bypass mutant of fission yeast hsk1. more...
Organism:
Schizosaccharomyces pombe
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL7715
7 Samples
Download data: CEL, TXT
Series
Accession:
GSE34369
ID:
200034369
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