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| Status |
Public on Feb 07, 2017 |
| Title |
Transcriptomic Profiling of 39 Neuroblastoma Cell Lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Harenza J, Diamond MA, Adams RN, Song MM, Davidson HL, Dent MH, Fortina P, Reynolds CP, Maris JM |
| Citation(s) |
28350380, 34818552 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 CA124709 |
The Genetic Basis of Neuroblastoma Tumorigenesis |
CHILDREN'S HOSPITAL OF PHILADELPHIA |
JOHN M MARIS |
| R01 CA180692 |
Role of LMO1 in Neuroblastoma Initiation and Maintenance |
CHILDREN'S HOSPITAL OF PHILADELPHIA |
JOHN M MARIS, A. THOMAS LOOK |
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| Submission date |
Nov 01, 2016 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Jo Lynne Rokita |
| E-mail(s) |
rokita@chop.edu
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| Organization name |
Children's Hospital of Philadelphia
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (41)
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| This SubSeries is part of SuperSeries: |
| GSE89969 |
Genomic Profiling of Neuroblastoma Cell Lines |
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| Relations |
| BioProject |
PRJNA352080 |
| SRA |
SRP092413 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89413_2016-10-30-NBL-cell-line-STAR-fpkm.txt.gz |
5.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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