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Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

Claire Marchal, Takayo Sasaki, Daniel Vera, Korey Wilson, Jiao Sima, Juan Carlos Rivera-Mulia, Claudia Trevilla García, Coralin Nogues, Ebtesam Nafie, David M. Gilbert
doi: https://doi.org/10.1101/104653
Claire Marchal
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Takayo Sasaki
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Daniel Vera
2Center for Genomic and Personalized Medicine, Florida State university, Tallahassee, Florida, USA
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Korey Wilson
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Jiao Sima
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Juan Carlos Rivera-Mulia
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Claudia Trevilla García
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Coralin Nogues
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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Ebtesam Nafie
3Zoology department, Benha university, Benha, Qalyubia, Egypt
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David M. Gilbert
1Department of Biological Science, Florida State University, Tallahassee, Florida, USA
2Center for Genomic and Personalized Medicine, Florida State university, Tallahassee, Florida, USA
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ABSTRACT

Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a rapid, robust and relatively inexpensive protocol to analyze genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing RT allelic asynchrony, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 01, 2017.
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Repli-seq: genome-wide analysis of replication timing by next-generation sequencing
Claire Marchal, Takayo Sasaki, Daniel Vera, Korey Wilson, Jiao Sima, Juan Carlos Rivera-Mulia, Claudia Trevilla García, Coralin Nogues, Ebtesam Nafie, David M. Gilbert
bioRxiv 104653; doi: https://doi.org/10.1101/104653
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Repli-seq: genome-wide analysis of replication timing by next-generation sequencing
Claire Marchal, Takayo Sasaki, Daniel Vera, Korey Wilson, Jiao Sima, Juan Carlos Rivera-Mulia, Claudia Trevilla García, Coralin Nogues, Ebtesam Nafie, David M. Gilbert
bioRxiv 104653; doi: https://doi.org/10.1101/104653

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