Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines - PubMed (original) (raw)

Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines

Jo Lynne Harenza et al. Sci Data. 2017.

Erratum in

Abstract

Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1

Figure 1. Experimental and data analysis workflow.

Cell lines were thawed and cultured to ~60–80% confluence before passaging and finally, pelleting. RNA was extracted, sequencing performed, and data analysis performed as described.

Figure 2

Figure 2. Validation of MYCN genomic amplification status in neuroblastoma cell lines.

Plotted are rank-ordered MYCN FPKM values for the human fetal brain sample and each cell line, colored by known MYCN copy number status. These data validate known MYCN amplification status for each cell line.

Figure 3

Figure 3. Concordance of differentially-expressed genes between neuroblastoma cell lines and primary tumors.

(a) Across the neuroblastoma cell lines, 3,940 genes were differentially-expressed (DE) based on MYCN amplification status and of those, 2,395 were differentially-expressed based on MYCN amplification status in primary tumors and were significantly correlated (Pearson’s R=0.824, P<2.2 e-16). (b) The fold changes of these DE genes were significantly correlated between the cell line dataset and the patient tumor dataset (Pearson’s R=0.73, P<2.2 e-16). (c) A significant correlation between the common 6,523 genes that were not DE in cell lines and tumors was observed (Pearson’s R=0.829, P<2.2 e-16). (d) As expected, correlation of the non-DE genes’ fold changes was close to zero (Pearson’s R=0.052, P<3 e-5).

References

Data Citations

    1. Harenza J., Diamond M. A., Hart L. S., Maris J. M. 2016. Gene Expression Omnibus . GSE89413
    1. 2009. NBCI Bioproject . PRJNA89523
    1. Harenza J., Diamond M. A., Maris J. M. 2016. Gene Expression Omnibus . GSE89968

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