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Of the 86 genes profiled by qRT-PCR, 66 were deemed detected by all three platforms and are displayed as individual dots in this figure.
In this analysis, 11 cell type-specific gene signatures for which three or more genes were detected by all three platforms were included.
Of note, 156 differentially expressed genes were identified by all three platforms to change in the same direction, representing 40% of the size of the smallest of the three lists (Fig. 1A).
Of the 86 genes profiled by qRT-PCR, 66 were deemed detected by all three platforms and were deemed truly differentially expressed with gestational age (A) and with labor at term (B) if significant by qRT-PCR analysis.
Furthermore, whether a dominant (sample A) or minor (sample C) group, gram-positive bacteria were detected by all three platforms with only minor variation between the three extraction methods.
After final design and library production, ∼1 Mb of genomic positions were physically targeted by all three platforms.
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Using the Ingenuity Pathway Analysis software (IPA) (Redwood City, CA) we carried out an analysis of the biological information retrieved by each of the individual platforms alone, and compared it to the information obtained by the integrated analysis of all three platforms.
We found that 75.8%% of these differentially expressed miRNAs were also present in our list of 98 miRNAs, (miRNAs detected by at least one sample on all three platforms; significant overlap, P = 5.11e-18, hypergeometest test, determined with the reference set of miRNAs as the panel of 800 assessed by NanoString).
The overall pattern is similar for all three platforms, as confirmed by the results displayed in Figure 1.
The global gene expression patterns of the six cell lines in all three platforms were studied by principal component analysis (PCA) [ 59].
The second aberration, a complex change towards the telomere of arm 5p, is also seen by all four platforms, but the clarity of the pattern is variable.
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