Mic array (South San Francisco, CA). All 1516647 PCR 
amplification reagents were purchased from Applied Biosystems, Inc. (Foster City, CA). Briefly, 50 ng of total RNA was reverse transcribed in a 15 ml reaction mixture containing 0.2 ml of 100 nM dNTP, 0.2 ml of RNase inhibitor 20 U/ml, 1.5 ml of reverse transcriptase (50 U/Multi-Platform Analysis of MicroRNA ExpressionAffymetrix. Raw data for cross-platform comparisons was extracted without normalization by using the miRNA QC Tool (Affymetrix, Santa Clara, CA). For the purpose of this study, the 847 human miRNA transcripts that are interrogated on Affymetrix miRNA Array 1.0 (miRBase 11.0) were analyzed. Signal intensities with p,0.06 were considered to be detected. Illumina. Data were extracted without background subtraction or normalization in a Sample Probe Profile format by using BeadStudio v3.4 (Illumina). The vendor provided miRNA detection threshold was p,0.05. For this platform, 858 miRNA transcripts were interrogated and available for detection. Agilent. Data was extracted using Agilent Feature Extraction Software v9.5 (Santa Clara, CA). Transcripts detectable by the Agilent platform had a standard error of three times the background. There were 719 miRNAs detectable on this 
platform. NanoString. Raw data was normalized using internal positive spike controls to account for variability in the hybridization process. The data was further normalized to the Epigenetic Reader Domain average Epigenetics counts of all endogenous miRNAs in each lane to account for any variability in the sample input. MiRNA detection was determined using a metric that yields a detection call at a confidence level of 95 (p,0.05). This detection measure identifies all miRNAs in which the count of the miRNA is two standard deviations above the average of negative spike probes. This platform interrogated 654 miRNA targets. miRNA-Seq. The sequence reads from the Illumina Genome Analyzers were aligned using the Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) algorithm. The Flicker (Illumina) tool was used for processing and initial analysis of miRNA sequencing data including the following steps: 1) trimming the known Illumina adaptor from the reads and exclusion of reads smaller than 15 bp. 2) Alignment of trimmed reads to the genome sequence targets using ELAND for length 15?0 bp. 3) The alignments are sequential in the order mature, iso, loop and then precursor, so a read mapping to mature miRNA is not considered for iso miRNAs. 4). Flicker results were parsed and reported as counts for the miRNA, and these counts were used for expression analysis. Following the primary analysis, counts were scaled by dividing the gene count by the total number of counts for each sample. Then, each data point for each sample was multiplied by the average of the total counts for all lanes. A threshold cutoff of five normalized counts was used as a detected transcript. All counts were then log2 transformed and used in the comparison studies. For purposes of this work, 792 transcripts were considered to be detectable using the miRNA-Seq platform. miRNA PCR. Multivariate analysis was used to pairwise compare miRNA fold-change values across each platform. The miRNA transcript RNU48 was used to normalize qPCR data (MiRNA Ct ?RNU48 Ct = D Ct) and each tissue sample was then calibrated to RNU48-normalized data from the cell line H1299 (Tissue DCt ?H1299 D Ct = DD Ct). Microarray, NanoString and MiRNA-Seq fold-change values represent thedifference in miRNA exp.Mic array (South San Francisco, CA). All 1516647 PCR amplification reagents were purchased from Applied Biosystems, Inc. (Foster City, CA). Briefly, 50 ng of total RNA was reverse transcribed in a 15 ml reaction mixture containing 0.2 ml of 100 nM dNTP, 0.2 ml of RNase inhibitor 20 U/ml, 1.5 ml of reverse transcriptase (50 U/Multi-Platform Analysis of MicroRNA ExpressionAffymetrix. Raw data for cross-platform comparisons was extracted without normalization by using the miRNA QC Tool (Affymetrix, Santa Clara, CA). For the purpose of this study, the 847 human miRNA transcripts that are interrogated on Affymetrix miRNA Array 1.0 (miRBase 11.0) were analyzed. Signal intensities with p,0.06 were considered to be detected. Illumina. Data were extracted without background subtraction or normalization in a Sample Probe Profile format by using BeadStudio v3.4 (Illumina). The vendor provided miRNA detection threshold was p,0.05. For this platform, 858 miRNA transcripts were interrogated and available for detection. Agilent. Data was extracted using Agilent Feature Extraction Software v9.5 (Santa Clara, CA). Transcripts detectable by the Agilent platform had a standard error of three times the background. There were 719 miRNAs detectable on this platform. NanoString. Raw data was normalized using internal positive spike controls to account for variability in the hybridization process. The data was further normalized to the average counts of all endogenous miRNAs in each lane to account for any variability in the sample input. MiRNA detection was determined using a metric that yields a detection call at a confidence level of 95 (p,0.05). This detection measure identifies all miRNAs in which the count of the miRNA is two standard deviations above the average of negative spike probes. This platform interrogated 654 miRNA targets. miRNA-Seq. The sequence reads from the Illumina Genome Analyzers were aligned using the Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) algorithm. The Flicker (Illumina) tool was used for processing and initial analysis of miRNA sequencing data including the following steps: 1) trimming the known Illumina adaptor from the reads and exclusion of reads smaller than 15 bp. 2) Alignment of trimmed reads to the genome sequence targets using ELAND for length 15?0 bp. 3) The alignments are sequential in the order mature, iso, loop and then precursor, so a read mapping to mature miRNA is not considered for iso miRNAs. 4). Flicker results were parsed and reported as counts for the miRNA, and these counts were used for expression analysis. Following the primary analysis, counts were scaled by dividing the gene count by the total number of counts for each sample. Then, each data point for each sample was multiplied by the average of the total counts for all lanes. A threshold cutoff of five normalized counts was used as a detected transcript. All counts were then log2 transformed and used in the comparison studies. For purposes of this work, 792 transcripts were considered to be detectable using the miRNA-Seq platform. miRNA PCR. Multivariate analysis was used to pairwise compare miRNA fold-change values across each platform. The miRNA transcript RNU48 was used to normalize qPCR data (MiRNA Ct ?RNU48 Ct = D Ct) and each tissue sample was then calibrated to RNU48-normalized data from the cell line H1299 (Tissue DCt ?H1299 D Ct = DD Ct). Microarray, NanoString and MiRNA-Seq fold-change values represent thedifference in miRNA exp.
