The midguts were manually dissected under a microscope and regions were separated by hand based on the anatomical features of the main midgut regions identified in Buchon et al 2013, Cell reports. More information on gut regions can be found at flygut.epfl.ch
In the infection data, we present fold induction of guts in infected conditions compared to unchallenged conditions. However if the gene was not originally detected in this cell type, but is now expressed, we refer to it as switched on. If the gene is expressed in basal conditions but no more detected upon infection, we refer to it as switched off. Also, when genes are regulated more than 1000 times, we refer to it as switched on or off, in order to still see milder regulation in different cell types.
This ratio is indicative of the RT-qPCR ratio you could measure with RpL32 (Rp49) as a reference gene.