ecDNA copy number heterogeneity

Neuroblastoma exhibits significant inter- and intra-tumour genetic heterogeneity and varying clinical outcomes. Here, we used DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. We reveal extensive intercellular ecDNA copy number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000727	Single-nuclei sequencing data from four neuroblastoma patients. Each patient was run on two lanes, resulting in two runs per patient. Data is provided in paired-end fastq files.	Illumina NovaSeq 6000	8
EGAD50000000728	Genomic and Transcriptomic single-cell sequencing of neuroblastoma patient. Data represents one 96-well plate that was processed with G&T sequencing, resulting in genomic and transcriptomic data from the same single cells. Dataset contains 95 bam files containing the DNA sequencing data and 95 bam files containing the RNA sequencing data.	Illumina NovaSeq 6000	190
EGAD50000000729	Genomic and Transcriptomic sequencing of neuroblastoma HSR and ecDNA cell lines. Data represents five 96-well plates that were processed with G&T sequencing, resulting in genomic and transcriptomic data from the same single cells. Dataset contains 95 bam files containing the DNA sequencing data and 95 bam files containing the RNA sequencing data of CHP212 cells, 380 bam files (190 DNA and 190 RNA) for TR14 cells, 188 bam files (94 DNA and 94 RNA) for Kelly cells and 192 bam files (96 DNA and 96 RNA) for IMR5/75 cells.	Illumina NovaSeq 6000	950