The RNA was recovered in RNase free water, heat denatured for 10 min.

at 65°C; Veliparib purchase quantified with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Rockland DE, USA) and a quality profile with the Agilent 2100 bioanalyzer (Agilent Technologies GmbH, Waldbronn, Germany) was made. CodeLink target labeling and array hybridization Target preparation was done using the “”CodeLink selleck products Expression Assay Reagent Kit”" Manual Prep (Amersham Biosciences, Chandler AZ, USA) and the original protocol for CodeLink System manual target preparation (Amersham Biosciences, Chandler AZ, USA). Briefly: 2 μg total RNA were used in cDNA synthesis reaction with a poly-A binding primer containing the T7-polymerase promoter. Clean up of the resulting dsDNA fragments was done using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). For target labeling the cDNA was in vitro transcribed by partially

substituting UTP with bio-16-UTP in the reaction mixture. Labeled cRNA was Anlotinib supplier purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany). Portions of 20 μg cRNA were subjected to fragmentation in the presence of Mg2+. Subsequently 10 μg fragmented cRNA (target) was loaded onto UniSet Human I BioArray glass slides (n = 2 arrays per sample) and hybridized for 18 h in a Minitron shaker incubator (Infors AG, Bottmingen, Germany) at 37C°/300 rpm. Washing and dyeing with Cy-5 coupled streptavidin

(Amersham Biosciences, Freiburg, Germany) was done according to the original protocol and the arrays were scanned using an GenePix 4000 B scanner and GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA). Microarray data analysis Images were analyzed using CodeLink Expression Analysis Software. Data was normalized by quantile normalization [38]. Data was log2 transformed and spots that were always flagged EMPTY were removed. Spots that were flagged empty across all technical replicates were discarded. Ureohydrolase All spots except the DISCOVERY spots were also discarded. The missing values were imputed using SeqKNN [39]. Technical replicates were averaged. Differentially expressed genes were detected using Rank Products [40], both at False Discovery Rate 5 and 10, as an unpaired analysis for each treatment being compared to the untreated control chips. The resulting gene list was subjected to DAVID and EASE [41] for annotation and overrepresentation analysis of gene categories. Due to the highly similar expression profiles of all donors to every single pathogen the microarray results presented in all tables are the mean fold change for the donor pool. The microarray data has been submitted to the ArrayExpress database and can be accessed using the accession number E-MEXP-1613.