Computational protocol: Modulation of the Host Interferon Response and ISGylation Pathway by B. pertussis Filamentous Hemagglutinin

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Protocol publication

[…] Arrays were scanned using a GenePix 4000b microarray scanner (Axon Instruments, Foster City, CA), and image analysis was performed using GenePix Pro version 5.0 (Axon Instruments). Data were expressed as the log2 ratio of background-subtracted fluorescence intensities from the sample versus the reference, for each element on the array . Data were filtered to retain only the elements with a signal/background intensity ratio >2.5 (in either sample or reference channel) in at least 80% of the 23 arrays, and with a regression correlation coefficient between sample and reference signal >0.6. Using these criteria, we identified 25,867 well-measured elements. The time course data from each treatment were normalized to the averaged time-zero data of four replicates. The data were hierarchically clustered using the CLUSTER program , and displayed using TREEVIEW (http://rana.lbl.gov/EisenSoftware.htm). […]

Pipeline specifications

Software tools GenePix Pro, TreeViewX
Application Phylogenetics
Organisms Bordetella pertussis, Homo sapiens
Diseases Muscular Diseases