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In parallel, we isolated RNA from each sample and constructed corresponding whole genome cDNA libraries.
To evaluate the performance of our peptide panel for separating SJIA flare from KD and FI, we used the discriminant analysis-derived prediction scores for each sample and constructed ROC curves [ 35, 36].
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After allowing 48 hrs for cell recovery, the cells were inoculated into 150 mm dishes at 6×105 cells/dish, corresponding to three to six dishes for each electroporated cell sample and construct.
Known groups validity was also demonstrated on the baseline sample, and construct validity was examined using principal components analysis and exploratory item response theory analysis.
We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments.
To demonstrate that all xenograft tumors were indeed RMS tumors, we collected tumor samples and constructed a xenograft tissue microarray (TMA) with adherent RD cells and corresponding sphere cultures as controls.
DLN and BE provided access to clinical data on study material, and EB and CLTJ collected the tissue samples and constructed the TMAs.
In addition to the full protein alignments, we built a separate alignment for PDZ domains (as in ref [ 2] but with an extended gene sampling) and constructed specific alignments for the SAM and SH3 domains of Shank.
We used high-throughput Illumina sequencing technology to conduct paired-end sequencing for DNA samples, and constructed a 500 bp library with extended data of 500 Mb, and a 6 kbp library with expected data of 250 Mb.
We left out one sample at a time, then used the remaining 79 samples to select the 5 antibodies with values increased in tumor patient samples according to the p-values for 2-sample T-tests of tumor vs. non-tumor samples, and constructed the resulting discriminant function based on the 79 samples.
Rainwater samples were collected using a purpose-built wet-only rain sampler designed and constructed at the Fatih University Department of Environmental Engineering.
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