title: Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR.
abstract: Long non-coding RNAs (lncRNAs) form a new class of RNA molecules implicated in various aspects of protein coding gene expression regulation. To study lncRNAs in cancer, we generated expression profiles for 1707 human lncRNAs in the NCI60 cancer cell line panel using a high-throughput nanowell RT-qPCR platform. We describe how qPCR assays were designed and validated and provide processed and normalized expression data for further analysis. Data quality is demonstrated by matching the lncRNA expression profiles with phenotypic and genomic characteristics of the cancer cell lines. This data set can be integrated with publicly available omics and pharmacological data sets to uncover novel associations between lncRNA expression and mRNA expression, miRNA expression, DNA copy number, protein coding gene mutation status or drug response.
authors.affiliation: Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Mestdagh
authors.affiliation: Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
authors.forename: Steve
authors.initials: S
authors.lastname: Lefever
authors.affiliation: Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
authors.forename: Pieter-Jan
authors.initials: PJ
authors.lastname: Volders
authors.affiliation: Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.
authors.forename: Stefaan
authors.initials: S
authors.lastname: Derveaux
authors.affiliation: Biogazelle, 9052 Zwijnaarde, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Hellemans
authors.affiliation: Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.|Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
authors.forename: Jo
authors.initials: J
authors.lastname: Vandesompele
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D062085:RNA, Long Noncoding