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Series GSE6977 Query DataSets for GSE6977
Status Public on Aug 14, 2007
Title Genome-wide Profiling of DNA Replication Timing in pombe.
Organism Schizosaccharomyces pombe
Experiment type Other
Summary DNA replication is initiated at multiple sites or origins enriched with AT-rich sequences at various times during the S-phase. While current studies of genome-wide DNA replication profiles have focused on the timing of replication and the location of origins, the efficiency of replication/firing at various origins remains unclear. In this study, we show different efficiencies of DNA replication at various loci by using ORF-specific DNA microarrays. DNA copy-number increases as a function of time at individual loci are approximated to near-sigmoidal models for estimation of replication initiation and completion timings in HU-challenged cells. Duplicating times (from initiation to completion) vary from loci to loci, partly contributing to various firing efficiencies at origins. DNA replication timing profiles are strikingly similar to the reported patterns of enriched ssDNA, suggesting that majority stalled forks are restored for resumption of DNA replication. Although the DNA replication timing profiles are disrupted in HU-challenged cds1? cells, ~85% of potential origins overlapped with those found in wild type cells, significantly, most of which represents inefficiently fired origins in wild type cells. Together, our result indicates that replication checkpoint plays a role in monitoring efficient origins and thus maintaining global DNA replication patterns in HU-challenged cells.
Keywords: WT or Cds1 HU synchronized cells released in HU free media and harvested at different time points vs WT or Cds1 synchronized with HU for 3 hrs.
 
Overall design We analyzed 32 arrays for WT and 38 arrays for Cds1 cells which were synchronized with HU and released in HU free media and harvested at different time points. At least two biological repeats were done for each time points.
 
Contributor(s) Eshaghi M, R. Krishna M. K, Li J, Chu Z, T. Liu E, Liu J
Citation(s) 17684567
Submission date Feb 07, 2007
Last update date Jan 18, 2013
Contact name Majid Eshaghi
E-mail(s) meshaghi@hotmail.com
Organization name Genome Institute of Singapore
Department Bilogical Investigation
Lab System Biology
Street address Biopolis
City Singapore
State/province Singapore
ZIP/Postal code 138672
Country Singapore
 
Platforms (1)
GPL1932 S. pombe 10K long oligonucleotide array
Samples (70)
GSM160745 SP HU syn WT harvested at 000 min Bio_1_R1
GSM160746 SP HU syn WT harvested at 000 min Bio_1_R2
GSM160747 SP HU syn WT harvested at 000 min Bio_2_R1
Relations
BioProject PRJNA99309

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE6977_RAW.tar 60.1 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table
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