Data Descriptor: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines Jo Lynne Harenza 1 , Maura A. Diamond 1 , Rebecca N. Adams 2 , Michael M. Song 3 , Heather L. Davidson 3 , Lori S. Hart 1 , Maiah H. Dent 1 , Paolo Fortina 2 , C. Patrick Reynolds 3 & John M. Maris 1,4 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. Design Type(s) cell type comparison design Measurement Type(s) transcription profiling assay Technology Type(s) RNA sequencing Factor Type(s) cell line Sample Characteristic(s) Homo sapiens • neuroblastoma cell line • epithelial cell line • embryonic brain 1 Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA. 2 Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA. 3 Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA. 4 Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA. Correspondence and requests for materials should be addressed to J.M.M. (email: maris@email.chop.edu). OPEN Received: 23 November 2016 Accepted: 7 February 2017 Published: 28 March 2017 www.nature.com/scientificdata SCIENTIFIC DATA | 4:170033 | DOI: 10.1038/sdata.2017.33 1