Flies were grown at 25°C on PB medium (KD Medical, Columbia, MD) for 3 to 5 days post eclosion. Adults were then collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).
Extracted molecule
total RNA
Extraction protocol
Adults were collected and quick frozen on dry ice and total RNA was extracted (Andrews et al, Genome Research 10:2030-2043) using Trizol reagent (GibcoBRL, Gaithersburg, MD).
Sample is from flies homozygous for protein-null Mnn1 alleles and is described in detail in Cerrato et al., Dev Biol. 2006 Oct 1;298(1):59-70.
Data processing
CEL files were processed using the Bioconductor Affy package, version 2.12.0 (Bolstad et al., 2003; Irizarry et al., 2003). The Robust Multichip Average (RMA) function was used to normalize intensities and extract expression value. Specifically, RMA implements a probe specific correction of the PM probes using a model based on observed intensity (the sum of signal and noise), followed by normalization of corrected PM probes using quantile normalization, and finally, calculation of expression measure using a median polish.
