title: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.
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.
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Jo Lynne
authors.identifier: 0000-0003-2171-3627
authors.initials: JL
authors.lastname: Harenza
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Maura A
authors.initials: MA
authors.lastname: Diamond
authors.affiliation: Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA.
authors.forename: Rebecca N
authors.initials: RN
authors.lastname: Adams
authors.affiliation: Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Song
authors.affiliation: Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA.
authors.forename: Heather L
authors.initials: HL
authors.lastname: Davidson
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Lori S
authors.initials: LS
authors.lastname: Hart
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Maiah H
authors.initials: MH
authors.lastname: Dent
authors.affiliation: Cancer Genomics and Bioinformatics Laboratory, Sidney Kimmel Cancer Center, Philadelphia, Pennsylvania 19107, USA.
authors.forename: Paolo
authors.initials: P
authors.lastname: Fortina
authors.affiliation: Cancer Center, Texas Tech University Health Sciences Center School of Medicine, Lubbock, Texas 79430, USA.
authors.forename: C Patrick
authors.initials: CP
authors.lastname: Reynolds
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.|Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Maris
mesh_terms: D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D006801:Humans; D009154:Mutation; D009447:Neuroblastoma / Q000235:genetics*