Hi Gil,
We have characterized the Drosophila replication program in three cell lines
(Kc167, S2-DRSC and ML-DmBG3-c2) by genome-wide profiling of 5-bromo-2-
deoxyuridine incorporation (early origins of replication) and Orc2 binding (ORC
sites). All data was deposited at GEO.
GSE17285, Kc167 Early origins of replication
GSE17286, S2-DRSC, Early origins of replication
GSE17287, ML-DmBG3-c2 Early origins of replication
GSE20887, ORC2 S2-DSRC ChIP-Seq
GSE20888, ORC2 MLDmBG3-c2 ChIP-Seq
GSE20889, ORC2KC-167 ChIP-Seq
As described in our Genome Research paper (FBrf0213065), to facilitate
inter-cell line comparisons of early origins, we assembled a single set of genomic
loci that had evidence for early origin activity in at least one of the three cell lines;
we refer to this as the set of early origin meta-peaks. Similarly, we assembled
a single set of ORC sites with evidence for Orc2 binding in at least one of the
three cell lines; we refer to this as the set of ORC meta-peaks. I've attached
GFF3 files for the early origin meta-peaks and the ORC meta-peaks. In the score
column I listed the fraction of the three cell lines that the peak had support in.
So, for example, if a peak existed only in Kc cells it got a 1/3, but if a meta-peak
overlapped an early origin peak in all three cell lines it got a 1.
The "attribute" (group) column is a little different between the two files. For the
ORC meta-peaks I gave each an arbitrary ID and then listed which cell lines they
appeared in, the exact format for peak "i" for example is:
ID=ORC-meta-i;peaks=BG3:TRUE/FALSE,Kc:TRUE/FALSE,S2:<up>TRUE/
FALSE</up>.
For the early origin meta-peaks, I listed the same thing but also included the
aggregated early origin tiling array score within the bounds of the early origins.
This is the value that we regressed on to in figure 4c of the paper. The TRUE/
FALSE classification was the subject of 4b.
ID=EO-meta-i;scores=BG3:<score>,Kc:<score>,S2:<score>;peaks=BG3:<up>TRUE/
FALSE</up>,Kc:TRUE/FALSE,S2:TRUE/FALSE.
Let me know if you have any questions about these files or if you'd like any other
data.
Best,
Matt