Project description:This data is a subset of the miRQC study, submitted for publication in summer of 2013. The purpose of the study was to compare various aspects of miRNA profiling platform performance (reproducibility, sensitivity, accuracy, etc) using a standardized set of samples. The data included in this submission is a subset of the study data generated on the Agilent miRNA profiling system. The array used was designed to measure all of the human and human viral miRNAs in miRBase 16.0 and the is annotated based on miRBase 18. Analysis for the miRQC study was based only on the human sequences present in miRBase 18 (8 sequences were deleted between 16.0 and 18.0)
Project description:This data is a subset of the miRQC study, submitted for publication in summer of 2013. The purpose of the study was to compare various aspects of miRNA profiling platform performance (reproducibility, sensitivity, accuracy, etc) using a standardized set of samples. The data included in this submission is a subset of the study data generated on the Agilent miRNA profiling system. The array used was designed to measure all of the human and human viral miRNAs in miRBase 16.0 and the is annotated based on miRBase 18. Analysis for the miRQC study was based only on the human sequences present in miRBase 18 (8 sequences were deleted between 16.0 and 18.0) miRNA profiling on a standardized set of 20 samples.
Project description:Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms. Keywords: cross platform microarrays
Project description:Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms. Keywords: cross platform microarrays
Project description:Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms. Keywords: cross platform microarrays
Project description:HepG2 cells were exposed to similar concentrations of BaP in two different laboratories (2.5 uM at Institute of Cancer Research and 3 uM at Maastricht University)for 6 and 24 h. Gene expression was analysed by Agilent oligonucleotide microarrays and Cancer Research UK (CR-UK) cDNA microarrays. An inter-laboratory and inter-platform comparison were performed on the data. Keywords: other