Project description:Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma. This SuperSeries is composed of the SubSeries listed below.

2019-11-03 | GSE138315 | GEO

Expression profiling in Neuroblastoma Primary tumors and Cell lines

Project description:Expression profiling in Neuroblastoma Primary tumors and Cell lines

2009-12-03 | GSE19274 | GEO

MYCN and MYC ChIP-Seq profiling in neuroblastoma cell lines

Project description:MYCN and MYC profiling in neuroblastoma cell lines

2019-11-03 | GSE138295 | GEO

Genome-wide SNP Profiling of 27 Neuroblastoma Cell Lines

Project description:We used SNP arrays to perform genome-wide profiling of commonly-used neuroblastoma cell lines.

2017-02-07 | GSE89968 | GEO

Genome-wide profiling of mature piRNAs in human Neuroblastoma (NB) cell lines

Project description:To elucidate potential role of piRNAs in Neuroblastoma (NB), we performed the genome wide profiling in two human NB cell lines, IMR-32 and SH-SY-5Y by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways. The RNA sequencing results revealed both known and novel piRNAs in both the cell lines. We observed a total 630 annotated mature piRNAs, distributed across chromosomes and mitochondria which were mapped to various genomic locations such as introns, protein coding regions, repeats, pseudogenes, ncRNAs etc. This is the first study reporting the extensive catalogue of human NB piRNAs which will provide a useful resource to dissect complex neoplastic events that are possibly mediated by piRNAs in neuroblastoma. Moreover, these piRNAs could be used as probable small RNA biomarkers for the Neuroblastoma.

2018-03-20 | GSE83945 | GEO

Transcriptomic Profiling of 39 Neuroblastoma Cell Lines

Project description: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.

2017-02-07 | GSE89413 | GEO

Neuroblastoma cell line profiling

Project description:24 standard human Neuroblastoma Cell lines were profiled without applying any transfections in order to measure the expression profiles. Keywords: cell line, neuroblastoma, mRNA profiling. This dataset can be visualized and analyzed in the R2 platform: http://r2.amc.nl

2013-03-16 | GSE28019 | GEO

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