Notes on array comparisons published in Lindell et al 2006
By Anne Thompson (12-18-08)

Raw array data is available through Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). There are nine timepoints and three replicates per timepoint. There are three arrays for every experimental treatment timepoint. Some of the control timepoints were averaged as described by Debbie in an email:'We found very little difference between the control cells for T=4 and T=8 hours so decided to save money and did not run arrays from T=5,6 or 7. Instead we averaged the results of T=4 and T=8 for the paired comparisons to the infected cells for T=5,6 and 7.'

The excel file in the GEO folder should have the key to which arrays belong to which treatment and experiment.

The .cel files in the folder currently labeled 'old' are the fullset of experimental treatment arrays for phage infection. I'm not sure who added those to the ftp site and why they did not add the control arrays as well.