Transcriptomic Profiling of 39 Neuroblastoma Cell Lines

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 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. This data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (eg: MYCN amplification status, ALK mutation status, 11q status, sensitivity to pharmacological pertubation). 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. We sequenced neuroblastoma cell lines (N=39) with varying genomic characteristics, disease stages, and phases of therapy. We also sequenced the hTERT-immortalized retinal pigmented epithelial cell line, RPE-1 (N=1), which is commonly used as a non-neuroblastoma control, as well as RNA from the fetal brain (N=1), which can serve as a non-neuroblastoma neural-cell derived control.