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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
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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.
Laser capture microdissection and microarray analysis These procedures were performed as described in Electronic supplementary material (ESM) Methods.
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.
Overall, a total of 59 RNA pools from 15 strains in 4 conditions were subjected to microarray analysis according to the procedures described [ 60].
For clonal assays, flow cytometry, annexin V staining, electroporation, RNA isolation, quantitative real-time PCR, and microarray analysis, see Supplemental Experimental Procedures.
To prepare the samples for microarray experiments the "GeneChip Expression Analysis" procedure of Affymetrix (Santa Clara, USA) was followed.
The procedure for microarray analysis was described earlier by our group [ 10].
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