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Benchmarking RNA sequencing sensitivity using transcriptome-wide RT-qPCR data

Jan Hellemans - Aug 26, 2014

In the US FDA-led SEQC (aka MAQC-III) study, different sequencing platforms were tested across more than ten sites using well established reference RNA samples with built-in truths in order to assess the discovery and expression profiling performances of platforms and analysis pipelines (Su, Łabaj, Li et al., Nature Biotechnology, 2014). The entire SEQC data set comprises over 100 billion reads (10 Tb) thus providing a unique resource for thorough assessment of RNA-seq performance. Biogazelle co-authored and complemented this study by defining the first human transcriptome using well-established RT-qPCR technology. Using almost 21,000 PrimePCR qPCR assays (jointly developed by Biogazelle and Bio-Rad), the mRNA expression repertoire of the four MAQC samples was established.

Topics: RNA sequencing- RT-qPCR- sensitivity- read depth

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