New 'origin of replication' and stranded RNA-seq tracks in GBrowse
As part of the modENCODE project, Eaton et al. have used two complementary approaches to characterize the replication program of Drosophila melanogaster. In one approach, regions of early replicating DNA were identified by BrdU labeling of stalled replication forks in cell lines. In a more high resolution approach, sites of ORC (Origin Recognition Complex) loading, representing potential origins of replication, were identified by chromatin immunoprecipitation of Orc2 from asynchronous cultured cells. FlyBase has incorporated this genome-wide analysis of the replication program in the "Origin of replication" GBrowse track, which displays both early replicating regions ("eORI") and "Orc2" sites. Look for this track with other "Mapped features" tracks in the "Tracks" selection menu at the bottom of the GBrowse page.
FlyBase has also just incorporated several new RNA-Seq data sets from the modENCODE project. These data sets differ from our current RNA-Seq data in that the expression is displayed by strand. One of these data sets includes temporal expression data from the embryonic stages. The other data sets include expression data from a selection of tissues and timepoints, and under a variety of treatments. RNA-Seq expression data, by strand, from cell lines (e.g. Kc, S2) is also now available.
The Treatment Data represents the transcriptome of 4-day old mated adult flies and/or feeding third instar larvae that were fed or exposed to various toxins or environmental stress factors encountered in nature. The concentrations and exposure times used in this study were taken from previously published experiments or were based on experimentally determined LD50 results when there were no preexisting data available. These data can be viewed on GBrowse by selecting the Data Source menu option “D. melanogaster RNA-Seq Data” and selecting the appropriate tracks.
Since this is a beta release of these data, we are soliciting feedback from users on the format and presentation. Please send your comments to us using the contact FlyBase form.