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Twelve significantly differentially expressed transcripts from the TLDA study were selected for a second verification in 13 new tumour samples using individual TaqMan assays (with primers and probes targeting the same region as in the TLDA study).
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Error awareness was indicated by a second (verification) button press.
As a first verification for the increase in power by simultaneously using the parallel screening structure, we resampled datasets, each consisting of a fixed number of siRNAs and pathogens, and fitted the PMM, respectively the Moderated T-Test (MTT) [ 36] for the case of one pathogen (see Methods for details).
Transcripts selected for the second verification are highlighted in bold.
For the second verification method, 15 DNA samples from the Coriell Cell Repository (Camden, NJ, USA) were genotyped using the Taqman™ assay.
The adjusted questionnaire was then sent to the experts for a second round of verification.
The identical TaqMan assays as present on the TLDA cards were ordered separately from Applied Biosystems for the the second verification study.
Two reviewers screened studies for eligibility; one reviewer extracted data from relevant studies and a second performed verification for accuracy and completeness on a 10% sample.
An updated mechanism of the dynamic tag keys is introduced and a self-synchronized scheme is designed in the protocol, which has achieved the second verification for the tags.
Moreover, the 89 genes selected for the first verification round are not included in MYC curated genesets from Molecular Signature Database (Broad Institute, ), seemingly the majority of differentially expressed transcripts verified in this study are not part of the MYCN downstream signalling network.
These methods are suitable for a first iteration in a verification to be performed in a short time on an already built plant.
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