Raw Expression Data and Model

Raw RNA-Seq expression data obtained from a N starvation time course experiment on C. reinhardtii wild type CC-3269 (Boyle et al. 2012, GEO data set GSE34585 ) was aligned with STAR to the current genome annotation (version 5.5 from Phytozome). Next, using cuffdiff, we computed for each transcript i at each time point t, the log2 expression ratio, r as,

ri (t) = log2 [ ( xi (t) +1 ) / (xi (t=0) +1)]

where xi (t) represents the expression in fragments per kilobase of transcript per million mapped reads (FPKM) of transcript i at time t. We filtered out unchanging transcripts and noisy expression measurements by selecting any transcript that complied with any of the following two rules: (1) ri (t) > abs (1) during the lipid accumulation time points, i.e., at time points 8 h, 12 h, 24 h and 48 h after N starvation or (2) consistent ri (t) > abs (1) for a single period of at least 30 min.

The matrix of r values for the 2,150 transcripts can be downloaded here.

Finally, if you are interested on the raw model and you would like to query it through scripting, here you can access a flat text version of the model.