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| Status |
Public on Nov 28, 2019 |
| Title |
New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
DNA replication must be faithful and follow a well-defined spatio-temporal program closely linked to genomic organization, transcription, epigenomic marks, intra-nuclear structures, mutation rate and cell fate determination. Replication timing (RT) analyses require complex, precise and time-consuming experimental procedures, and the study of large-size computer files. We improved the RT protocol to speed up and increase its quality and reproducibility. We partly automated the RT protocol via the IP-star robot (Diagenode) and developed a user-friendly software: the START-R suite (Simple Tool for the Analysis of the Replication Timing based on R). START-R suite is an open source software using an R script and an HTML interface to analyse DNA replication timing in a given cell line from microarray or deep-sequencing results. This new approach can be used by every biologist without specific knowledge in bioinformatics and reduces the time required for generating and analyzing data from several samples simultaneously. START-R suite detects constant timing regions (CTR) but also, and it is a novelty, it identifies temporal transition regions (TTR) and significant differences between two experimental conditions. The informatic global analysis requires less than 10 minutes.
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| |
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| Overall design |
Nascent-DNA from early S-phase versus nascent-DNA from late S-phase.
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| |
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| Contributor(s) |
Hadjadj D, Denecker T, Guérin E, Kim SJ, Fauchereau F, Baldacci G, Maric C, Cadoret JC |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 27, 2019 |
| Last update date |
Nov 30, 2019 |
| Contact name |
Jean-Charles Cadoret |
| E-mail(s) |
jean-charles.cadoret@ijm.fr
|
| Organization name |
CNRS/ Université de Paris
|
| Street address |
15 rue hélène Brion
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
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| Platforms (2) |
| GPL10123 |
Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version) |
| GPL10152 |
Agilent-021924 SurePrint G3 Human CGH Microarray 8x60K (Feature Number version) |
|
| Samples (7)
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| GSM4195540 |
180k K562 new cell sorting method replication timing |
| GSM4195541 |
K562 180k old cell sorting method replication timing |
| GSM4195542 |
Manual1 U2OS replication timing |
|
| Relations |
| BioProject |
PRJNA592170 |
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