Dan Koboldt (from massgenomics) has posted about what I know to be the 1st independent look at the data from Ion Torrent's 316 chip,
Granted the data was handed to him in a 'shiny report with color images' but he has bravely ignored that to give an honest look at the raw data itself.
The 316 chip gives a throughout that nicely covers WGS reseq experiments for bacterial sized genomes. "The E. coli reference genome totals about 4.69 Mbp. With 175 Mbp of data, the theoretical coverage is around 37.5-fold across the E. coli genome."
For those wary of dry reviews, fear not, easily comprehensible graphs are posted within!
read the full post here
Showing posts with label real-time PCR. Show all posts
Showing posts with label real-time PCR. Show all posts
Tuesday, 12 July 2011
Wednesday, 2 March 2011
Papers on Comparison of microRNA profiling platforms
Systematic Evaluation of Three microRNA Profiling Platforms: Microarray, Beads Array, and Quantitative Real-Time PCR Array
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
Background
A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA).
Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.
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