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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Human and Mouse Cells Time of Replication (ToR)

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE17229: Mouse Cells Time of Replication (ToR) GSE17235: Human Cells Time of Replication (ToR) Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Itamar Simon

PROVIDER: E-GEOD-17236 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

Yaffe Eitan E Farkash-Amar Shlomit S Polten Andreas A Yakhini Zohar Z Tanay Amos A Simon Itamar I

PLoS genetics 20100701 7

Recent evidence suggests that the timing of DNA replication is coordinated across megabase-scale domains in metazoan genomes, yet the importance of this aspect of genome organization is unclear. Here we show that replication timing is remarkably conserved between human and mouse, uncovering large regions that may have been governed by similar replication dynamics since these species have diverged. This conservation is both tissue-specific and independent of the genomic G+C content conservation. ...[more]

PMID: 20617169

Similar Datasets

Mouse Cells Time of Replication (ToR)

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

Human Cells Time of Replication (ToR)

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

rnai tor time course - The signalization way TOR/PTEN in Arabidopsis

Project description:gnp_blan06_torpten - rnai tor time course - The impact of the TOR pathway on growth and stress responses. Modification of translational and transcriptional profiles in Tor-inducible RNAi mutants and identification of TOR targets. 28 dye-swaps - normal vs. rnai mutant comparison.

2011-01-07 | E-GEOD-25701 | biostudies-arrayexpress

dark hypocotyls tor rnai-Dark hypocotyls TOR RNAi

Project description:fapesp-bra-inra-10-01_bioen_hypocotyl - dark hypocotyls tor rnai - Transcriptional comparison between 2 TOR RNAi mutants versus GUS control. - Sowing after 24h imbibition at 4M-BM-0C in the dark, on MS1/5, no sucrose, 10 mM ethanol, 8 g/l agar, vertical growth with 3h light, 6 days growth in the dark (20M-BM-0C), hypocotyls were harvested under green light ; cotyledons and root were removed. 4 dye-swap - normal vs rnai mutant comparaison

2012-10-10 | E-GEOD-41404 | biostudies-arrayexpress

Vibrio cholerae: Wild type El Tor biotype versus crp mutant

Project description:Transcriptional profiling of an El Tor biotype crp mutant The virulent V. cholerae El Tor Ogawa strain C7258 (Peru isolate 1991) and an isogenic deletion mutant (WL7258) lacking DNA sequences encoding the cAMP receptor protein were grown in LB medium to optical density at 600 nm of 1.5. The cultures were chilled in ice, cells quickly collected by centrifugation and total RNA imediately extracted. RNAwas extracted and purified using the Trizol plus RNA purification system (Invitrogen) followed RNEasy miniElute cleanup (Qiagen). RNA samples were conserved at - 80 C and used within a week. 4 replicates

2010-05-27 | E-GEOD-7519 | biostudies-arrayexpress

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Project description:gnp_blan06_torpten - lst8 - The impact of the TOR pathway on growth and stress responses. Comparison between the lst8 mutant vs. WT in short day and in long day conditions. 8 dye-swaps - gene knock out.

2010-12-08 | E-GEOD-25731 | biostudies-arrayexpress

Overexpression of pten2a: The signaling pathway of TOR/PTEN in Arabidopsis

Project description:gnp_blan06_torpten - overexpression of pten2a - The impact of the TOR pathway on growth and stress responses. - Comparaison control versus overexpressor. The overexpressor has a male phenotype of sterility. 3 dye-swap - gene knock in (transgenic)

2010-11-30 | E-GEOD-24902 | biostudies-arrayexpress

rnai tor time course - The signalization way TOR/PTEN in Arabidopsis

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Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication

Project description:Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex DUP-TRP/INV-DUP rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM#300260) and Pelizaeus-Merzbacher disease (PMD, MIM#312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals M-bM-^@M-^S 16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homologyM-bM-^@M-^Tor homeologyM-bM-^@M-^Tdriven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication, and potentially higher order amplification of a genomic interval, can occur in a manner consistent with rolling circle amplification as predicted by the microhomology mediated break induced replication (MMBIR) model. To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the Xq22 chromosomal region to query the genomic DNA of 7 males with Pelizaeus-Merzbacher disease, and 5 unaffected or carrier/unaffected family members. A 4x44k Agilent Technologies (Santa Clara, CA) microarray was designed using the Agilent e-array website targeting the region of the genome encompassing the dosage-sensitive PLP1 gene.

2014-11-25 | E-GEOD-63594 | biostudies-arrayexpress

tor-Transcriptome analysis of TOR (Target of Rapamycin) mutant.

Project description:ra03-07_tor - tor - Study of 2 TOR mutants (7817 Strong, 7846 weak) - Mutant vs wild type on different nitrogen conditions (10mM=control and 100uM) Keywords: treated vs untreated comparison,wt vs mutant comparison

2007-06-20 | GSE7987 | GEO

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