3d gene human microrna oligo chip

Total miRNA was extracted from 300 μl aliquots of serum samples using the 3D-Gene^® RNA extraction reagent from a liquid sample kit (Toray Industries, Inc., Kanagawa, Japan). Comprehensive miRNA expression analysis was performed using a 3D-Gene^® microRNA Labeling kit and a 3D-Gene^® Human microRNA Oligo Chip (Toray Industries, Inc.), designed to detect 2540 miRNA sequences registered in miRBase releases 20 and 21 (http://www.mirbase.org/). MiRNA was defined as present if the corresponding microarray signal was more than the signal (mean + 2 × standard deviations) of the negative controls, of which the top and bottom 5%, ranked by signal intensity, were considered noise generated by the experimental system and were removed. When the signal value was negative, or undetected, after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale. Three pre-selected internal control miRNAs (miR-149-3p, miR-2861, and miR-4463) were used to normalize signals across the different microarrays tested. The results were subjected to probability analysis using receiver operating characteristic curves. All microarray data of this study are in agreement with the Minimum Information About a Microarray Experiment (MIAME) guidelines and are publicly available through the GEO database (GSE134108, http://www.ncbi.nlm.nih.gov/projects/geo/).

Comprehensive microRNA expression analysis was performed using the 3D-Gene human microRNA oligo chip (Toray Industries, Inc., Japan), which was designed to detect 2,565 microRNAs registered in miRBase release 21 (http://www.mirbase.org/). Similarly, comprehensive mRNA expression analysis was performed using the 3D-Gene human oligo chip 25K manual (v. 2.01). The microarray data signals were treated similarly as previously described [3 (link)]. To normalize signals across the different microarrays, quantile normalization was applied. Numeric analyses were performed using R v. 3.1.2 (R foundation for Statistical Computing, http://www.R-project.org). All microarray data from this study are in agreement with the Minimum Information about a Microarray Experiment standard and are publicly available through the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/projects/geo/) under accession number GSE114318.