GEO DataSets

(Submitter supplied) DNA replication is very well orchestrated in mammalian cells due to a tight regulation of the temporal order of replication origin activation, known as the replication timing program. The replication timing of a given replication domain is very robust and well conserved in each cell type. Upon low replication stress, the slowing of replication forks induces delayed replication of some fragile regions leading to DNA damage and genetic instability. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL10123

37 Samples

Download data: BED, TXT

(Submitter supplied) RKO cells were treated with low doses of aphidicolin (0.2µM) that inhibit replicative DNA polymerases and induce a mild replication stress. ATAC-seq data were analysed on control cells (DMSO) and after 16h of treatment with aphidicolin

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BED, BW

(Submitter supplied) RKO cells were treated with low doses of aphidicolin (0,2µM) that inhibit replicative DNA polymerases and induce a mild replication stress. Expression data were analysed on control cells (DMSO), 16h of treatment (t0) and after release in complete new culture medium of 13h (N+1) using microarray (affymetrix Clarion S) We used microarray to analyse the impact of low replication stress on gene expression comparing DMSO or aphidicolin-treated cells at the end of the treatment (t0) and in daughter cells released from the replication stress (N+1).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

12 Samples

Download data: CEL

(Submitter supplied) DNA is replicated in a defined temporal order termed the replication timing (RT) program, which is correlated with genome compartmentalization with early replicating chromatin located mainly in the A compartment and late replicating chromatin in the B compartment (Dixon et al 2012, Moindrot et al 2012, Ryba et al 2010, Yaffe et al 2010). Similarly, active histone modifications and transcriptional permissiveness are associated with early replication while a repressive chromatin state is associated with late replication (Hiratani et al 2009, Riveria-Mulia et al 2015, Lubelsky et al 2014). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

156 Samples

Download data: BIGWIG, BW, COOL, MAT, TXT

(Submitter supplied) Replication timing (RT) associates with genome architecture, while having a mixed relationship to histone marks. By profiling replication at high-resolution and systematically assessing broad and focused histone marks across cell cycle with and without genetic perturbation, we address the causal relationship between histone marks, their associated states and RT. Our approach identified four chromatin states, including a previously uncharacterized H3K36me2 state, that defined 97% of the mappable genome. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL16791

252 Samples

Download data: BED, BIGWIG

(Submitter supplied) Replication timing (RT) control is linked to histone modifications (HMs) and genome architecture. However, HM landscape across cell cycle and its relationship with RT and chromatin modifiers have not been comprehensively assessed. Here we perform detailed replication profiling together with cell cycle profiling of multiple HMs, ATAC-seq, and gene expression. We classify 97% of the genome into four gross chromatin states, including a previously uncharacterized intergenic H3K36me2 state. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

28 Samples

Download data: BIGWIG

(Submitter supplied) Replication timing (RT) control is linked to histone modifications (HMs) and genome architecture. However, HM landscape across cell cycle and its relationship with RT and chromatin modifiers have not been comprehensively assessed. Here we perform detailed replication profiling together with cell cycle profiling of multiple HMs, ATAC-seq, and gene expression. We classify 97% of the genome into four gross chromatin states, including a previously uncharacterized intergenic H3K36me2 state. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

208 Samples

Download data: BED, BIGWIG

(Submitter supplied) Diploid human cell lines were treated with aphidicolin as a model to see how DNA replication stress affects the genome, by identifying which copy number alterations appear in the first cell cycle. RNAseq was used to see whether there is any link between loci with recurrent CNAs and gene transcription in the genes located there.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) We profiled replication timing in Suz12 knockout ESCs and observed no differences relative to wild-type controls.

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL11620

2 Samples

Download data: PAIR

(Submitter supplied) Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

25 related Platforms

993 Samples

Download data: BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, PAIR, TSV, TXT

(Submitter supplied) DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

1 Sample

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL16791 GPL11154 GPL20795

35 Samples

Download data: BED, BW

(Submitter supplied) DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

24 Samples

Download data: BW

(Submitter supplied) DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL16791

10 Samples

Download data: BED

(Submitter supplied) We report Repli-Seq analysis of the replication program in human lymphoblasts grown in the absence or in the presence of aphidicolin, an inhibitor of replicative DNA polymerases used in vitro to destabilize CFSs. We identified regions displaying specific replication delay upon aphidicolin treatment, resulting in under-replication. We then further study the mechanisms leading to such specific delayed/under-replication within CFSs and show that transcription-dependent segregation of initiation events out of the gene body generates long-traveling forks in large transcribed domains, which elicits the replication timing delay responsible for CFS instability upon replication stress.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

30 Samples

Download data: BW

(Submitter supplied) The entire genome is divided into distinct 1-2 Mb zones that replicate in an ordered and coordinated manner during S phase. While most regions of the genome replicate both alleles in a synchronous manner, some loci have been found to replicate asynchronously, with one allele undergoing DNA synthesis early in S phase, with the other replicating during late S. Random asynchronous replication timing is characterized by cell heterogeneity with some cells. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

15 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) We replaced the endogenous histones of Drosophila melanogaster with either histones containing an H3K9R mutation or histones containing an H4K16R mutation to interrogate established genome-wide correlations between chromatin state, transcription, and DNA replication timing. We performed total RNA-seq in H4K16R males and females to investigate the role of H4K16 in dosage compensation of the male X chromosome. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17275

30 Samples

Download data: TXT

(Submitter supplied) To detect transcripts before and after APH treatment, we subjected total RNA isolated from U2OS cells expressing human FANCD2-3xFLAG to next generation sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TSV

(Submitter supplied) Genome-wide distribution of FANCD2 protein in chromatin under replication stress.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: WIG