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We used SPM99b (Wellcome Department of Cognitive Neurology) implemented in MATLAB (Mathworks Inc., Natick, MA) installed on UNIX workstations (SGI, Mountain View, CA) for initial data processing and subsequent statistical analysis.
RNA extraction, hybridization and initial data processing and normalization were performed as previously described [ 39].
TC and YZ did the initial data processing and quality control assessment.
Initial data processing and integration were conducted using HKL2000, with the resolution limits determined by inspection.
The gene expression module of the BeadStudio software version 3.1 (Illumina) was used for initial data processing and background correction.
We also employed computer programs in structured query language (SQL) for initial data processing and sample selection.
Initial data processing and base calling, including extraction of cluster intensities, was done using RTA 1.12.4 (HiSeq Control Software 1.4.5 Illuminaa).
RL wrote the computer scripts for primer design and initial data processing, gave informatics support, and contributed to data evaluation.
The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.
designed the hybrid capture probe set, S.K. and B.T. performed the sequencing and initial data processing, K.C. provided support with analysis strategy.
All experimental protocols, primer sequences, and the scripts for primer design and initial data processing are available from our website [ 29].
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