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Series GSE137764 Query DataSets for GSE137764
Status Public on Sep 20, 2019
Title High Resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116 as well as F1 sub-species hybrid mouse embryonic stem cells and their neural progenitor derivatives. Strong enrichment of nascent DNA in fine temporal windows reveals a remarkable degree of cell to cell conservation in replication timing and patterns of replication genome-wide. We identify 5 patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation were found throughout S phase and resolved to ~50kb precision. Temporal transition regions were resolved into segments of uni-directional replication punctuated with small zones of inefficient initiation. Small and large valleys of convergent replication were consistent with either termination or broadly distributed initiation, respectively. RT correlated with chromatin compartment across all cell types but correlations of initiation time to chromatin domain boundaries and histone marks were cell type specific. Haplotype phasing revealed previously unappreciated regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchrony was associated with large transcribed genes that resemble common fragile sites. Altogether, these data reveal a remarkably deterministic temporal choreography of DNA replication in mammalian cells.
Overall design 85 Samples
Contributor(s) Zhao PA
Citation(s) 32209126
Submission date Sep 19, 2019
Last update date Mar 29, 2020
Contact name David M Gilbert
Organization name Florida State University
Department Department of Biological Science
Street address 319 Stadium Drive
City Tallahassee
State/province FL
ZIP/Postal code 32301
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (85)
GSM4086849 H1_G1_WGS
GSM4086850 H1_S1_BrdU
GSM4086851 H1_S2_BrdU
BioProject PRJNA566530
SRA SRP222591

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Supplementary file Size Download File type/resource
GSE137764_H1_GaussiansGSE137764_mooth_scaled_autosome.mat.gz 6.0 Mb (ftp)(http) MAT
GSE137764_H1_IZs_hg38.bed.gz 17.2 Kb (ftp)(http) BED
GSE137764_H9_GaussiansGSE137764_mooth_scaled_autosome.mat.gz 5.2 Mb (ftp)(http) MAT
GSE137764_HCT_GaussiansGSE137764_mooth_scaled_autosome.mat.gz 4.5 Mb (ftp)(http) MAT
GSE137764_mESC_Gaussiansmooth_scaled_autosome.mat.gz 4.8 Mb (ftp)(http) MAT
GSE137764_mNPC_Gaussiansmooth_scaled_autosome.mat.gz 5.0 Mb (ftp)(http) MAT
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