N starvation comparisons published in Tolonen et al 2006, Molecular Systems Biology.
Notes by Anne Thompson (12-18-08)

Raw data is available for this experiment through Array Express. There is also a description of the samples that were compared and the experimental design at Array Express. The excel spreadsheet in this folder contains a key for the file names, treatments, and timepoints of the samples as they are named through Array Express. The way they are named in this folder is pretty obvious.

It wasn't obvious from the paper so I wanted to summarize which arrays were compared to each other for MIT9313. For MED4, the comparisons were fairly obvious with a control vs. experimental comparison made between each timepoint.  The cyanate and urea treatments were compared to the arrays labeled as ammonium treatment.

For MIT9313, 24hour control arrays were either not used for some reason or not available. The expression values in the N array paper for t24 are the result of comparing t24 minus N(reps 1 and 2) to the control for 12 hours.

For MIT9313, expression values for urea were reached through comparison of the urea treatment with t3 plusN rep2 and t0 plusN rep1. The nitrite arrays were also compared to t3 plusN rep2 and t0 plusN rep1.

Hope this helps!
Anne