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The results obtained from the microarray analysis described the stable detection and reproducible results of the miR-638 expression level in plasma.
Microarray analysis (described in more detail in the following section) showed that the transcript levels of Ring1b and Phc1/Mph1 were significantly downregulated over time, and correspondingly decreased in protein levels (Figure 3A, Table S1).
The western blot procedure was also run using the pre-immune serum for a comparison with the immune serum and all samples were analysed using a rabbit anti-β tubulin polyclonal antibody as a control since the corresponding gene was not significantly different between the ranks in the microarray analysis described above.
The study is a verification of the results from a microarray analysis described previously [ 22].
Total RNA extraction was the same as that used for microarray analysis described above.
The list of significantly regulated genes selected by the microarray analysis described above was loaded in IPA with the following criteria: Reference set: HumanRef-8 v2.0; Direct and Indirect relationships included; filtered by species (human), and in a second round, by tissue (skeletal muscle).
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For H. polymorpha, Oh et al., [ 42] presented a partial, DNA microarray study, followed by a full DNA microarray analysis describing the transcriptional response of H. polymorpha to exposure to cadmium [ 43].
Most interestingly, the microarrays analysis described in this paper uncovers new MGF and MGFR and/or describes for the fist time expression patterns of well known MGF.
Since intergenic SVs with breakpoints mapping to the promoter region (398/1061) cannot be qualitatively distinguished using the RNA-Seq data, they were not part of the RNA-Seq analysis but are included in the microarray expression analysis described below.
The method for the miRNA microarray analysis was described in our previous report, except for the addition of an updated miRNA probe set (the NCode Human miRNA Microarray Probe Set V3+, Invitrogen) composed of 703 known and 393 predicted human miRNAs in the present work (Yu et al, 2007).
In this study, to investigate the role of TAMs in ESCC, we extracted the upregulated genes reported as M2 genes in MΦ-like THP-1 cells by conditioned medium of ESCC cell line with a cDNA microarray analysis as described.
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