Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]

ABSTRACT: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]

PROVIDER: PRJNA471506 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12058300_1.fastq.gz	Fastqsanger.gz
	SRR12058300_2.fastq.gz	Fastqsanger.gz
	SRR12058400_1.fastq.gz	Fastqsanger.gz
	SRR12058400_2.fastq.gz	Fastqsanger.gz
	SRR12058500_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1519

Similar Datasets

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]

Project description:In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages.

2019-06-26 | GSE114470 | GEO

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

Project description:Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

| PRJNA454731 | ENA

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq]

Project description:Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq]

| PRJNA454725 | ENA

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq]

Project description:Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq]

| PRJNA454741 | ENA

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [BrdU-IP Repli-chip]

Project description:Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [BrdU-IP Repli-chip]

| PRJNA464246 | ENA

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [RNA-seq]

2019-06-26 | GSE113983 | GEO

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq]

2019-06-26 | GSE113981 | GEO

scRepli-seq analysis of aphidicolin treated embryos

Project description:To analyze chromosome abnormalities of 8-cell embryos with/without aphidicolin treatment, we performed single cell replication sequencing (scRepli-seq). This submission is similar to our submission GSE226309.

2024-06-24 | GSE255456 | GEO

Genome-wide stability of DNA replication program in single mammalian cells

Project description:We report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

2018-12-13 | GSE108556 | GEO

Single-cell DNA replication sequencing (scRepli-seq): a method for mapping replication timing domains genome wide in single mammalian cells

Project description:Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require a large number of S-phase cells for either effective enrichment of replicating DNA through BrdU immunoprecipitation or the determination of copy number differences during S-phase, which restricts their application to non-abundant cell types. Here, we provide a simple, cost-effective, and robust protocol for single-cell DNA replication sequencing (scRepli-seq). The scRepli-seq methodology relies on the whole-genome amplification (WGA) of genomic DNA (gDNA) from single S-phase cells and next-generation sequencing (NGS)-based determination of copy number differences that arise between replicated and unreplicated DNA. We also provide computational pipelines that are key components of the methodology. NGS library preparation takes 3 d.

2020-10-07 | GSE138634 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data