
DOI . ORG {
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Title[redir]:
Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines | Scientific Data
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 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. Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Keywords {🔍}
cell, lines, neuroblastoma, data, article, rna, expression, google, scholar, cancer, gene, cas, nature, sequencing, line, mycn, performed, analysis, cat, genes, status, scientific, amplification, table, number, tumors, andor, differential, rnaseq, analyses, tumor, growth, download, fpkm, profiling, maris, sample, metadata, human, medium, cells, patient, correlated, pearsons, content, brain, research, genomics, quality, files,
Topics {✒️}
nature portfolio /marislab/nbl-cell-line-rna-seq privacy policy org/packages/release/bioc/html/genomicfeatures childhood cancer research methyl-cpg-binding domain sequencing /alexdobin/star/releases/tag/star_2 neuroblastoma research community therapeutically applicable research nature biotechnol 34 advertising nature 469 nature gov/programs/target/data-matrix social media research progress differentially-expressed genes’ log2-transformed index reprints author information authors single-nucleus atac sequencing real-time pcr analysis high-quality rna-seq dataset providing access /broadinstitute/picard/releases/tag/1 long-noncoding rna analysis high-throughput sequencing techniques author correspondence high-output flow-cell raw rna-sequencing data dnase-seq/atac-seq fetal brain rna isa-tab format /star-fusion/star-fusion jar collectinsertsizemetrics input=aligned describe transcriptome-wide profiling serum-free neurobasal medium matched patient-derived xenograft library preparation gene-level mrna abundances differential expression analyses patient-derived xenograft model11 thermo fisher scientific correlating fold-change yields normal brain tissue permissions data descriptor rna-seq data cog-derived cell lines common differentially-expressed genes
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headline:Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
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 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.
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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headline:Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines
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 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.
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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