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Chip hybridizations of at least two independent biological replicates for each treatment were performed at the Deutsches Ressourcenzentrum für Genomforschung (Berlin) using protocols recommended by Affymetrix.
For each independent biological replicate hybridization, fluorescently labeled targets from each experimental time point and the reference pool were combined and hybridized on an automated slide processor (GE Healthcare) using protocols recommended by the manufacturer.
The purified amplicon mixtures were sequenced by 454 FLX Titanium pyrosequencing using 454 Life Sciences primer A by the Genomics Resource Center at the Institute for Genome Sciences, University of Maryland School of Medicine, using protocols recommended by the manufacturer as amended by the Center.
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In previous studies for shake flask cultures, the commonly used protocol recommended by Invitrogen [ 10] for methanol feeding has been modified individually depending on the product.
Commercial ELISAs (USCN, Wuhan, China) targeting potential severity markers were used to measure in duplicate the levels of the proteins in individual DF and SD plasma specimen, using the protocols recommended by the manufacturer.
All arrays were performed using standard protocols recommended by the manufacturer within the UCLA DNA Microarray Facility.
RNA amplification, cDNA labelling and hybridization from XTC.UC1 cells were performed using the protocols recommended by the Transcriptome Core Facility (http://cardioserve.nantes.inserm.fr/ptf-puce/).
Lung function tests were performed using the protocols recommended by ATS/ERS guidelines [ 10].
The titer and percentage of recombinant phages in the library were determined using the protocols recommended by the manufacturer.
IL-5 and IL-13 concentrations were determined by two-site sandwich ELISAs, using the protocols recommended by the antibody suppliers.
Genomic DNA samples from patients and unaffected sibs from families MD1 and MD2, and a control sample were hybridized to GeneChip® Human Mapping 10 K XbaI 142 2.0 arrays (Affymetrix, Santa Clara, CA, USA) using the protocols recommended by the manufacturer.
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