title: Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.
abstract: Whole-transcriptome sequencing ('RNA-Seq') has been drastically changing the scale and scope of genomic research. In order to fully understand the power and limitations of this technology, the US Food and Drug Administration (FDA) launched the third phase of the MicroArray Quality Control (MAQC-III) project, also known as the SEquencing Quality Control (SEQC) project. Using two well-established human reference RNA samples from the first phase of the MAQC project, three sequencing platforms were tested across more than ten sites with built-in truths including spike-in of external RNA controls (ERCC), titration data and qPCR verification. The SEQC project generated over 30 billion sequence reads representing the largest RNA-Seq data ever generated by a single project on individual RNA samples. This extraordinarily ultradeep transcriptomic data set and the known truths built into the study design provide many opportunities for further research and development to advance the improvement and application of RNA-Seq.
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Xu
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Zhenqiang
authors.initials: Z
authors.lastname: Su
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Huixiao
authors.initials: H
authors.lastname: Hong
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland 20814, USA.
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland 20814, USA.
authors.forename: Danielle
authors.initials: D
authors.lastname: Thierry-Mieg
authors.affiliation: Chair of Bioinformatics Research Group, Boku University Vienna , Vienna, Austria ; University of Warwick , Coventry CV4 7AL, UK.
authors.forename: David P
authors.initials: DP
authors.lastname: Kreil
authors.affiliation: Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College , New York, New York 10021, USA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.affiliation: Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA ; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards; D006801:Humans; D011786:Quality Control; D012313:RNA / Q000235:genetics*; D012015:Reference Standards; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012313:RNA