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Comment
. 2016 Jul 5:3:160052.
doi: 10.1038/sdata.2016.52.

Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR

Pieter Mestdagh  1   2 , Steve Lefever  1   2 , Pieter-Jan Volders  1   2 , Stefaan Derveaux  1 , Jan Hellemans  3 , Jo Vandesompele  1   2
Affiliations
Comment

Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR

Pieter Mestdagh et al. Sci Data. .

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.

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Conflict of interest statement

Primer sequences are property of Biogazelle and non-exclusively licensed to WaferGen Biosystems.

Figures

Figure 1
Figure 1. Data generation workflow.
RNA isolated from NCI60 cell lines was reverse transcribed and profiled using 1707 lncRNA assays on a SmartChip system.
Figure 2
Figure 2. Technical validation of the lncRNA profiling platform.
(a) Mean Cq-values of 92 lncRNA assays in function of the molecule concentration used in the standard dilution series. Error bars represent the standard deviation of replicate measurements. (b) Distribution of efficiencies for all 92 assays. (c) Cq-correlation plot for replicate MAQC samples. Assays with Cq-value>28 in one or both replicates were set to 28 and color coded red. (d) MAQC titration response curve showing the percentage of titrating assays in relation to the expression difference between MAQCA and MAQCB.
Figure 3
Figure 3. Validation of the NCI60 lncRNA expression data.
(a) Hierarchical clustering of NCI60 cell lines according to the lncRNA expression data. Cancer types are color-coded. LncRNA expression values are shown as a heatmap. (b) Hierarchical clustering of NCI60 cell lines according to public mRNA expression data. (c) Expression of ANRIL and PVT1 in cell lines with differential ANRIL and PVT1 copy number.
See this image and copyright information in PMC

Comment on

  • Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study.
    Mestdagh P, Hartmann N, Baeriswyl L, Andreasen D, Bernard N, Chen C, Cheo D, D'Andrade P, DeMayo M, Dennis L, Derveaux S, Feng Y, Fulmer-Smentek S, Gerstmayer B, Gouffon J, Grimley C, Lader E, Lee KY, Luo S, Mouritzen P, Narayanan A, Patel S, Peiffer S, Rüberg S, Schroth G, Schuster D, Shaffer JM, Shelton EJ, Silveria S, Ulmanella U, Veeramachaneni V, Staedtler F, Peters T, Guettouche T, Wong L, Vandesompele J. Mestdagh P, et al. Nat Methods. 2014 Aug;11(8):809-15. doi: 10.1038/nmeth.3014. Epub 2014 Jun 29. Nat Methods. 2014. PMID: 24973947
  • Melanoma addiction to the long non-coding RNA SAMMSON.
    Leucci E, Vendramin R, Spinazzi M, Laurette P, Fiers M, Wouters J, Radaelli E, Eyckerman S, Leonelli C, Vanderheyden K, Rogiers A, Hermans E, Baatsen P, Aerts S, Amant F, Van Aelst S, van den Oord J, de Strooper B, Davidson I, Lafontaine DL, Gevaert K, Vandesompele J, Mestdagh P, Marine JC. Leucci E, et al. Nature. 2016 Mar 24;531(7595):518-22. doi: 10.1038/nature17161. Nature. 2016. PMID: 27008969

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References

Data Citations

    1. Mestdagh P., Vandesompele J. 2016. Gene Expression Omnibus. GSE80332

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