Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Measuring DNA replication timing of maize root tips using DNA copy number (S/G1) method with an EdU lableing step for bivariate sorting of S and G1 phase

ABSTRACT: DNA replication is a highly regulated cell cycle process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. We use both DAPI and 5-ethynyl-2'-deoxyuridine (EdU) labeling to perform fluorescence activated nuclei sorting (FANS) in combination with high throughput sequencing to characterize the patterns of DNA replication across the maize B73 genome using a DNA copy number based procedure.

ORGANISM(S): Zea mays

PROVIDER: GSE287258 | GEO | 2025/04/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

EDU-IP-MS of ecDNA positive and negative human COLO320, HEK293T and U251 cell lines

Project description:In this study, we established ecDNA-containing cell models by either transfecting synthetic circular DNA or excising endogenous chromosomal DNA. We found that ecDNA can be stable maintained in these cell models. By identifying proteins on nascent DNA, we found DNA damage repair pathway was significantly enriched in ecDNA-containing cells. ecDNA can activate DNA damage response. Further evidence show that TOP2B and LIG3. The association of ecDNA replication with cell proliferation and DNA damage response was explored by comprehensive profiling and analysis. Utilizing EdU (5-ethynyl-2’-deoxyuridine)-immunoprecipitation-mass spectrometry (EdU-IP-MS), we identified critical regulators involved in ecDNA replication and examined their functional roles in cancer cell DNA damage response and proliferation.

2025-04-18 | PXD060725 | Pride

Measuring DNA replication timing of maize root tips using DNA copy number (S/G1) method

Project description:During the cell cycle, DNA replication is a highly regulated process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. We are using fluorescence activated nuclei sorting in combination with high throughput sequencing to characterize the patterns of DNA replication across the maize B73 genome using a DNA copy number based procedure.

2025-04-29 | GSE287085 | GEO

Quantifying DNA replication speeds in single cells by scEdU-seq

Project description:In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2′-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

2024-04-19 | GSE211037 | GEO

Measuring DNA replication timing of maize root tips with Repli-seq method

Project description:DNA replication is a highly regulated cell cycle process that integrates the time that a genome segment replicates in S phase with its transcriptional activity, chromatin structure, and epigenetic state. The overall goal of this project is to define such linkages in maize by exploiting the genetic and genomic resources of this species. We used an updated Repli-seq protocol to profile replication timing in Zea mays B73 root tips and compare it to other methods for profiling replication timing.

2025-04-28 | GSE288800 | GEO

Measuring DNA replication timing of maize root tips with Repli-seq method

Project description:Measuring DNA replication timing of maize root tips with Repli-seq method

| PRJNA1219493 | ENA

Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

Project description:The ability to analyze chromatin accessibility at the single-nucleus level is a critical step towards capturing the highly complex mechanisms that regulate gene expression in the human brain, and to functionally characterize the genetic architecture of neuropsychiatric traits. The assay for transposase accessible chromatin (ATAC-seq) has rapidly established itself as a robust means of studying epigenome regulation in bulk tissues and, more recently, at the single-cell level. To facilitate optimal preparation of frozen archival human brain tissue samples for single-nuclear ATAC-seq (snATAC-seq), we assessed the impact of different sample preparation approaches on the quality of snATAC-seq libraries. We tested six conditions, including different fluorescent activated nuclear sorting (FANS) strategies, from nuclei isolated from a sample of human cortical tissue. Using an unbiased computational approach, we were able to identify major cell populations in all snATAC-seq libraries, including those not subjected to FANS. When FANS was used, we observed that the choice of DNA stain impacts the quality of ATAC-seq libraries. Staining samples with DAPI can lead to insufficient detection of open chromatin regions, whereas 7aad provides improved identification of some nuclear sub-populations. We also observed that use of fluorescent dyes (in particular, DAPI) can lead to under-sampling of excitatory neurons. Our work provides guidelines on the trade-offs associated with different nuclear isolation strategies when preparing samples for snATAC-seq.

2022-01-29 | GSE166016 | GEO

Vibert2017 - Tcell proliferation model

Project description:model allows us to infer proliferation rates and cell cycle phase durations from complex experimental 5-ethynyl-2'-deoxyuridine (EdU) data, revealing T cell proliferation heterogeneity and specific signatures. Model is encoded by Matthew Maire and submitted in BioModels by Krishna Kumar Tiwari.

2020-03-17 | MODEL2003170002 | BioModels

Differentially regulted genes in neural stem cells treated by oleanolic acid

Project description:Oleanolic acid significantly inhibited neurosphere formation in a dose-dependent manner, and achieved a maximum effect at 10 nM. OA also reduced the 5-ethynyl-2’-deoxyuridine (EdU) incorporation into NSCs, indicating an inhibition on proliferation of NSCs. Next, in western blotting analysis, the protein expression of neuron-specific marker tubulin-βⅢ (TuJ1) and Mash1 was increased, while the astrocyte-specific marker glial fibrillary acidic protein (GFAP) decreased. In immunofluorescence analysis, OA significantly elevated the percentage of TuJ1-positive cells and reduced GFAP-positive cells. Using DNA microarrays, 183 genes were found to be differentially regulated by OA.

2012-06-02 | GSE38394 | GEO

Differentially regulted genes in neural stem cells treated by oleanolic acid

Project description:Oleanolic acid significantly inhibited neurosphere formation in a dose-dependent manner, and achieved a maximum effect at 10 nM. OA also reduced the 5-ethynyl-2M-bM-^@M-^Y-deoxyuridine (EdU) incorporation into NSCs, indicating an inhibition on proliferation of NSCs. Next, in western blotting analysis, the protein expression of neuron-specific marker tubulin-M-NM-2M-bM-^EM-" (TuJ1) and Mash1 was increased, while the astrocyte-specific marker glial fibrillary acidic protein (GFAP) decreased. In immunofluorescence analysis, OA significantly elevated the percentage of TuJ1-positive cells and reduced GFAP-positive cells. Using DNA microarrays, 183 genes were found to be differentially regulated by OA. Neural stem cells derived form mouse embrynic brains were treated with Oleanolic acid or not. Each group had 4 biological relicates each from a mouse.

2012-06-01 | E-GEOD-38394 | biostudies-arrayexpress

Cohesin modulates DNA replication to preserve genome integrity [EdU-BrdU]

Project description:Cohesin participates in loop formation by extruding DNA fibers from its ring-shaped structure. Cohesin dysfunction eliminates chromatin loops but only causes modest transcription perturbation, which cannot fully explain the frequently observed mutations of cohesin in various cancers. Here, we found that DNA replication initiates at more than one thousand extra dormant origins after acute depletion of RAD21, a core subunit of cohesin, resulting in earlier replicating timing at approximately 30% of the human genomic regions. In contrast, CTCF is dispensable for suppressing the early firing of dormant origins that are distributed away from the loop boundaries. Furthermore, greatly elevated levels of gross DNA breaks and genome-wide chromosomal translocations arise in RAD21-depleted cells, accompanied by dysregulated replication timing at dozens of hotspot genes. Thus, we conclude that cohesin coordinates DNA replication initiation to ensure proper replication timing and safeguards genome integrity.

2022-07-31 | GSE189760 | 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