Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Replication maps of developing C. elegans embryos.

ABSTRACT: Okazaki fragments were purified and sequenced from C. elegans embryos at various stages of development. The sequencing data was used to map the positions and efficiencies of replication origins.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE90939 | GEO | 2016/12/15

SECONDARY ACCESSION(S): PRJNA356401

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Replication maps of HCT116 cells grown under various conditions

Project description:Okazaki fragments were purified and sequenced from HCT116 cells. The sequencing data were used to infer sites and efficiencies of replication initiation and termination.

2022-03-04 | GSE175938 | GEO

Replication maps of RPE-1 cells grown under various conditions

Project description:Okazaki fragments were purified and sequenced from RPE-1 cells. The sequencing data were used to infer sites and efficiencies of replication initiation and termination.

2018-11-01 | GSE114017 | GEO

Separable recruitment of DNA Polymerase α for leading- and lagging-strand replication initiation

Project description:Okazaki fragments were purified and sequenced from asynchronous S. cerevisiae at various DNA polymerase alpha levels in the presence or absence of interactions with Ctf4. The sequencing data was used to quantify efficiencies of replication origins.

2018-06-16 | GSE115897 | GEO

Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae

Project description:We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication. Examination of the distribution of Okazaki fragments in Saccharomyces cerevisiae strain S288C.

2013-06-18 | E-GEOD-42929 | biostudies-arrayexpress

Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae

2013-06-18 | GSE42929 | GEO

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

Project description:Short nascent strands purification coupled to next-generation sequencing allowed us to identify replication origins on human genome in an extensive way, by mapping replication origins in 4 different cell types, IMR-90 fibroblasts, hESC H9 cells, iPSC Th Cl-4 cells and HeLa cells. We demonstrated the existence of a cell type-specific reprogrammable signature of the cell identity revealed by specific efficiencies of conserved origin positions and not by the selection of cell-type specific subsets of origins. 4 different cell types were analyzed. For each cell types, 2 different biological replicates of short nascent strands at replication origins were purified. Each SNS sample was sequencing at least one time.

2012-07-01 | E-GEOD-37757 | biostudies-arrayexpress

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

2012-07-01 | GSE37757 | GEO

Quantitative, genome-wide analysis of eukaryotic replication initiation and termination

2013-02-28 | GSE40696 | GEO

Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).

Project description:Genome-wide replication fork directionality measured by strand-specific sequencing of Okazaki fragments in chicken lymphoma cells (DT40).

2022-02-18 | GSE196761 | GEO

Quantitative, genome-wide analysis of eukaryotic replication initiation and termination

Project description:Via the deep-sequencing of Okazaki fragments from Saccharomyces cerevisiae, we report the first comprehensive documentation of genome-wide replication directionality in any eukaryote; this permits the systematic analysis of both replication initiation and termination. We conduct a genome-wide analysis of origin competence and efficiency, and conclude that the majority of origins are competent to fire in each cell cycle and generally do so with high efficiency. Additionally, the spatial resolution of our data allow us to determine that leading-strand initiation generally occurs within the nucleosome-free region at origins. Using a strain in which late origins can be induced to fire early, we show that replication termination is a largely passive phenomenon that does not rely on cis-acting sequences or replication fork pausing and that the replication profile is determined largely by the kinetics of origin firing, allowing us to reconstruct chromosome-wide timing profiles from an asynchronous culture. 5 samples are included. Two are replicate, paired-end, wild-type samples sequenced via Illumina methodology. The raw data for these two are also deposited in the GEO repository under accession numbers GSM835650 and GSM835651. Two replicate, single-end, Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) overexpression via galactose induction experiments are reported sequenced via Ion Torrent methodology. One single-end, Sld2, Sld3, Dbf4, Dpb11, Cdc45 and Sld7 (SSDDCS) normal expression control via glucose media experiment is reported sequenced via Ion Torrent methodology.

2013-02-28 | E-GEOD-40696 | biostudies-arrayexpress

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