Niversal primers. The resulting PCR products were purified, applied to HumanRef-8 v3 beadchips (Illumina), and then hybridized for 16 h at 58uC. The beadchips were washed and then scanned in a BeadArray Reader using BeadScan v3 software (Illumina). Quality control parameters were determined to be within normal ranges before proceeding to the final data reduction. Raw, non-normalized, Illumina intensity values were used to compare across platforms.ml), 8 ml of 96-plex reverse primer (Applied Biosystems); mixed to allow a final concentration of 0.05X of each) and 1.6 ml of dH2O. Fifty nanograms of total RNA was added to the reaction mixture and incubated as follows; 16uC for 30 min, 42uC for 30 min and then 85uC for 5 min. Pre-amplification of cDNA was then initiated by creating a pool of 96 Title Loaded From File TaqMan miRNA Assays at a final concentration of 0.2X for each assay. The pre-PCR amplification reaction was performed in a 10 ml reaction mixture containing 5 ml TaqMan PreAmp Master Mix (2X), 2.5 ml of 96-pooled TaqMan assay mix (0.2X) and 2.5 ml of cDNA. The pre-amplification PCR was performed according to the following cycling conditions: one cycle 95uC for 10 min, 10 cycles at 95uC for 15 sec and then 60uC for 4 min. After pre-amplification PCR, the product was diluted 1:5 with dH2O and stored at 280uC until needed for amplification. Quantitative PCR of the miRNA targets was carried out using the 96.96 dynamic array (Fluidigm Corporation, CA, USA) following manufacturer’s protocol. Briefly, a 5 ml sample mixture was prepared for each sample containing 1x TaqMan Universal Master Mix (No UNG), 1X GE Sample Loading Reagent (Fluidigm PN 85000746) and each of diluted pre-amplified cDNA. Five microliters of assay mix were prepared with 1X each of TaqMan miRNA assay and 1X Assay Loading Reagent. The dynamic array was primed with control line fluid in the IFC controller and samples and 16574785 assay mixes were loaded into the appropriate inlets. The chip was then returned to the IFC controller for loading and mixing, and then placed in the BioMark Instrument for PCR at 95uC for 10 min, followed by 40 cycles at 95uC for 15 sec and 60uC for 1 min. The data was analyzed with Real-Time PCR Analysis Software in the Biomark instrument (Fluidigm Corporation, CA).Small RNA 24195657 SequencingOne microgram of total RNA sample was treated according to manufacturer’s instructions for the Small RNA v1.5 Sample Preparation (Illumina, San Diego, CA). As part of this procedure the small RNA libraries were enriched with 12 cycles of PCR prior to purification on a 6 polyacrylamide gel and excision of the 90?110 bp fraction using GeneCatcher gel tips (San Title Loaded From File Francisco, CA). The size-selected libraries were run on an Agilent 2100 Bioanalyzer to assess purity and quantitate the miRNA-enriched sample. Samples were diluted and clustered onto single read flow cells using either the Illumina Cluster Station or cBot. Sample containing flow cells were applied to the Illumina GAIIX (FF1, FFPE9a, and H1299-1) or HiSeq 2000 (FF2, FFPE9b, and H1299-2; San Diego, CA) instruments for sequencing-by-synthesis using standard Illumina reagents.NanoString nCounter AnalysisTotal RNA samples were analyzed according to manufacturer’s instructions for the nCounter Human miRNA Expression Assay kit (NanoString, Seattle, WA). Briefly, 100 ng of each total RNA sample was used as input into the nCounter Human miRNA sample preparation. Hybridization was conducted for 16 h at 65uC. Subsequently, the strip tubes were plac.Niversal primers. The resulting PCR products were purified, applied to HumanRef-8 v3 beadchips (Illumina), and then hybridized for 16 h at 58uC. The beadchips were washed and then scanned in a BeadArray Reader using BeadScan v3 software (Illumina). Quality control parameters were determined to be within normal ranges before proceeding to the final data reduction. Raw, non-normalized, Illumina intensity values were used to compare across platforms.ml), 8 ml of 96-plex reverse primer (Applied Biosystems); mixed to allow a final concentration of 0.05X of each) and 1.6 ml of dH2O. Fifty nanograms of total RNA was added to the reaction mixture and incubated as follows; 16uC for 30 min, 42uC for 30 min and then 85uC for 5 min. Pre-amplification of cDNA was then initiated by creating a pool of 96 TaqMan miRNA Assays at a final concentration of 0.2X for each assay. The pre-PCR amplification reaction was performed in a 10 ml reaction mixture containing 5 ml TaqMan PreAmp Master Mix (2X), 2.5 ml of 96-pooled TaqMan assay mix (0.2X) and 2.5 ml of cDNA. The pre-amplification PCR was performed according to the following cycling conditions: one cycle 95uC for 10 min, 10 cycles at 95uC for 15 sec and then 60uC for 4 min. After pre-amplification PCR, the product was diluted 1:5 with dH2O and stored at 280uC until needed for amplification. Quantitative PCR of the miRNA targets was carried out using the 96.96 dynamic array (Fluidigm Corporation, CA, USA) following manufacturer’s protocol. Briefly, a 5 ml sample mixture was prepared for each sample containing 1x TaqMan Universal Master Mix (No UNG), 1X GE Sample Loading Reagent (Fluidigm PN 85000746) and each of diluted pre-amplified cDNA. Five microliters of assay mix were prepared with 1X each of TaqMan miRNA assay and 1X Assay Loading Reagent. The dynamic array was primed with control line fluid in the IFC controller and samples and 16574785 assay mixes were loaded into the appropriate inlets. The chip was then returned to the IFC controller for loading and mixing, and then placed in the BioMark Instrument for PCR at 95uC for 10 min, followed by 40 cycles at 95uC for 15 sec and 60uC for 1 min. The data was analyzed with Real-Time PCR Analysis Software in the Biomark instrument (Fluidigm Corporation, CA).Small RNA 24195657 SequencingOne microgram of total RNA sample was treated according to manufacturer’s instructions for the Small RNA v1.5 Sample Preparation (Illumina, San Diego, CA). As part of this procedure the small RNA libraries were enriched with 12 cycles of PCR prior to purification on a 6 polyacrylamide gel and excision of the 90?110 bp fraction using GeneCatcher gel tips (San Francisco, CA). The size-selected libraries were run on an Agilent 2100 Bioanalyzer to assess purity and quantitate the miRNA-enriched sample. Samples were diluted and clustered onto single read flow cells using either the Illumina Cluster Station or cBot. Sample containing flow cells were applied to the Illumina GAIIX (FF1, FFPE9a, and H1299-1) or HiSeq 2000 (FF2, FFPE9b, and H1299-2; San Diego, CA) instruments for sequencing-by-synthesis using standard Illumina reagents.NanoString nCounter AnalysisTotal RNA samples were analyzed according to manufacturer’s instructions for the nCounter Human miRNA Expression Assay kit (NanoString, Seattle, WA). Briefly, 100 ng of each total RNA sample was used as input into the nCounter Human miRNA sample preparation. Hybridization was conducted for 16 h at 65uC. Subsequently, the strip tubes were plac.
