ArticleNature protocols2011
Genome-scale analysis of replication timing: from bench to bioinformatics.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
87 citing papers in PubMed.
- Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control.Nature communications · 2026Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- REPLAY: A reproducible and user-friendly application for DNA replication timing analysis from Repli-seq data.bioRxiv : the preprint server for biology · 2026Article
- The inverse relationship between copy number variation burden and age of onset of metabolic syndrome in Korean middle-aged adults.BMC medical genomics · 2026Article
- DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A.PLoS genetics · 2026Article
- DNA methylation and lncRNA control asynchronous DNA replication at specific imprinted gene domains.Nature communications · 2026Article
- Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine.Nucleic acids research · 2026Article
- ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis.Interdisciplinary sciences, computational life sciences · 2025Article
- ecDNA replication is disorganized and vulnerable to replication stress.Nucleic acids research · 2025Article
- Evaluating topography of mutational signatures with SigProfilerTopography.Genome biology · 2025Article
- Article
- High-fidelity, large-scale targeted profiling of microsatellites.Genome research · 2024Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses.Science advances · 2024Article
- MLL3/MLL4 enzymatic activity shapes DNA replication timing.bioRxiv : the preprint server for biology · 2023Article
- Repli-seq Sample Preparation using Cell Sorting with Cell-Permeant Dyes.Current protocols · 2023Article
- Replication dynamics identifies the folding principles of the inactive X chromosome.Nature structural & molecular biology · 2023Article
- H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins.Nature structural & molecular biology · 2023Article
- The location and development of Replicon Cluster Domains in early replicating DNA.Wellcome open research · 2023Article
- Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Replication timing profiles are cell type-specific and reflect genome organization changes during differentiation. In this protocol, we describe how to analyze genome-wide replication timing (RT) in mammalian cells. Asynchronously cycling cells are pulse labeled with the nucleotide analog 5-bromo-2-deoxyuridine (BrdU) and sorted into S-phase fractions on the basis of DNA content using flow cytometry. BrdU-labeled DNA from each fraction is immunoprecipitated, amplified, differentially labeled and co-hybridized to a whole-genome comparative genomic hybridization microarray, which is currently more cost effective than high-throughput sequencing and equally capable of resolving features at the biologically relevant level of tens to hundreds of kilobases. We also present a guide to analyzing the resulting data sets based on methods we use routinely. Subjects include normalization, scaling and data quality measures, LOESS (local polynomial) smoothing of RT values, segmentation of data into domains and assignment of timing values to gene promoters. Finally, we cover clustering methods and means to relate changes in the replication program to gene expression and other genetic and epigenetic data sets. Some experience with R or similar programming languages is assumed. All together, the protocol takes ∼3 weeks per batch of samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.