Projects

This page contains GenPlay projects available for downloads. This projects illustrate the type of data analysis and visualization that can be done with GenPlay. There are two sections: the first one contains projects that were used as supplementary data of articles published in scientific journals. The second section contains the projects created for the Tutorial section of this website.

How to start a project

You first need to download and install GenPlay from the Downloads page. Then, you need to download the project you want to launch. Once the download is finished, double click on the project file to start GenPlay and load the project. Loading a project might take a few minutes.

Projects from published work

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

Abstract

We have developed a new approach based on TimEX-seq to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronously replications. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. We show that the longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed timing wrinkles, which are previously undetected, highly reproducible, variations of the timing of replication in the 100kb-range that exist within the well-characterized megabase-sized replication timing domains. We show that these wrinkles correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequency during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.

Article

Coming soon.

GenPlay Project

Timing_and_NS_Profiles_2014.gppf

Identification of a BET Family Bromodomain/Casein Kinase II/TAF-Containing Complex as a Regulator of Mitotic Condensin Function

Abstract

Condensin is a central regulator of mitotic genome structure with mutants showing poorly condensed chromosomes and profound segregation defects. Here, we identify NCT, a complex comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), casein kinase II (CKII), and several TAFs, as a regulator of condensin function. We show that NCT and condensin bind similar genomic regions but only briefly colocalize during the periods of chromosome condensation and decondensation. This pattern of NCT binding at the core centromere, the region of maximal condensin enrichment, tracks the abundance of acetylated histone H4, as regulated by the Hat1-Mis16 acetyltransferase complex and recognized by the first Nrc1 bromodomain. Strikingly, mutants in NCT or Hat1-Mis16 restore the formation of segregation-competent chromosomes in cells containing defective condensin. These results are consistent with a model where NCT targets CKII to chromatin in a cell-cycle-directed manner in order to modulate the activity of condensin during chromosome condensation and decondensation.

Article

http://www.cell.com/cell-reports/fulltext/S2211-1247(14)00063-1

GenPlay Project

Kim_CellRep_2014.gppf

Projects from tutorials

ChIP-Seq Tutorial

Goal

The objective of this tutorial is to illustrate how GenPlay can be used to isolate peaks from the data generated from a ChIP-Seq experiment. Then, to generate a list of genes that have a peak in their promoter and finally to associate the score of the peak summit with each promoter.

Tutorial

ChIP-Seq Tutorial

Project File

Coming Soon