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Series GSE211037 Query DataSets for GSE211037
Status Public on Apr 19, 2024
Title Quantifying DNA replication speeds in single cells by scEdU-seq
Organism Homo sapiens
Experiment type Other
Summary 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.
 
Overall design Single cell analysis of Replication fork speeds over different treatment and knockouts.
Web link https://www.nature.com/articles/s41592-024-02308-4
 
Contributor(s) van den Berg J, van Batenburg V, van Oudenaarden A
Citation(s) 38886577
Submission date Aug 11, 2022
Last update date Jul 19, 2024
Contact name Jeroen van den Berg
E-mail(s) [email protected]
Phone +31610597913
Organization name Hubrecht Institute
Lab van Oudenaarden lab
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (50)
GSM6447737 RPE-1 hTERT FUCCI double pulse dT45min_1
GSM6447738 RPE-1 hTERT FUCCI double pulse dT45min_2
GSM6447739 RPE-1 hTERT FUCCI double pulse dT45min_3
Relations
BioProject PRJNA868727

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Supplementary file Size Download File type/resource
GSE211037_RAW.tar 2.3 Gb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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