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Series GSE141122 Query DataSets for GSE141122
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.
Overall design Nascent-DNA from early S-phase versus nascent-DNA from late S-phase.
Contributor(s) Hadjadj D, Denecker T, Guérin E, Kim SJ, Fauchereau F, Baldacci G, Maric C, Cadoret JC
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Submission date Nov 27, 2019
Last update date Nov 30, 2019
Contact name Jean-Charles Cadoret
Organization name CNRS/ Université de Paris
Street address 15 rue hélène Brion
City Paris
ZIP/Postal code 75013
Country France
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)
GSM4195540 180k K562 new cell sorting method replication timing
GSM4195541 K562 180k old cell sorting method replication timing
GSM4195542 Manual1 U2OS replication timing
BioProject PRJNA592170

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141122_RAW.tar 333.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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