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Microarray analysis procedures used here have been previously described (Gosse et al. 2008; Kozul et al. 2008).
Expression of 10 genes (A2m, Afp, Hamp2, Reep5, Slc39a5, Spink3, Alas2, Epor, Gata1, Klf1) was confirmed using the tissues from Study 2 by quantitative RT-PCR, validating our microarray analysis procedures.
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Detailed microarray analysis procedure and data processing are described under www.mh-hannover.de/rcut-downloads.html L=1.html L=1
Laser capture microdissection and microarray analysis These procedures were performed as described in Electronic supplementary material (ESM) Methods.
Despite the wealth of microarray time-series analysis procedures devised to date (such as [ 12, 13]), only simple linear regression methods are used in analyzing microarray data generated from most of the published ageing studies (for example, [ 3, 5, 7- 9]).
Salmonella microarray slide preparation and general microarray analysis followed the procedures described by Porwollik et al. [63].
Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays were used for microarray analysis and experimental procedures were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual.
PD performed the microarray analysis, all experimental procedures associated with the transcriptomic study, and wrote the first draft of the manuscript.
Such changes might, on one hand, be restricted to the microarray technology (e.g., modification or addition of sequences to a microarray, changes in data analysis procedures).
The microarray labeling, hybridization and analysis procedures were described previously in detail [ 19].
Overall, a total of 59 RNA pools from 15 strains in 4 conditions were subjected to microarray analysis according to the procedures described [ 60].
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