This page contains data files associated with Ni, Bruce et al, (2009,
Genes & Development).
- processed data.
The data processed as detailed in Materials and Method of the paper.
Files with names in the form of TF_30min.clean.null_norm.sig.sgr are
processed signal files for transcription factor TF at 30min in the sgr
format (chr, position, signal), suitable for viewing with IGB.
Files ending with the extension .prob.sgr contain data for the
probability that the red signal from all the probes in a band-width of
375 nucleotides is greater than the green signal due to chance. Files
with names like TF_30min.clean.null_norm.hits.q01.out list the location
of the signal peaks ("hits"), their average signal, and the
names of the flanking ORFs on the W and C strands, and whether the hit
is within an ORF. The hyperlink for each peak links to the ORF map at
the yeastgenome.org site.
- qPCR data. Contains the data necessary
to normalize the time points for Sko1 and Yap4 binding. For logistical
reasons each time point of the ChIP-chip assay was
done on a separate day. In order to ensure that the datasets are
normalized relative to each other, a smaller scale experiment was done,
all in one day, by performing ChIP qPCR on a small number of
chromosomal sites. The binding values determined by qPCR was plotted
for that determined by ChIP chip so as to generate a calibration curve
for each ChIP chip assay. The ChIP chip data for each time point was
multiplied by a correction factor that equalized the calibration curves.
- Expression data. Contains expression
data for wt (t=7.5, 15, 22.5, 30, 45 and 60 min post salt induction),
yap4-KO (t=0, 15, 30 and 45 min), yap6-KO (t=0,15,30 and 45min) and
yap4-KO/yap6-KO (t=0, 15, 30 and 45 min) . Each data file is for a two channel
hybridization experiment, where channel 2 (532) contains cDNA from wt_0min.