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Berlin Neuroblastoma single-cell DAC

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Dr Kerstin Haase
k.haase@ucl.ac.uk

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This DAC controls 6 datasets

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
EGAD50000001513	Single-cell G&T seq from an untreated PDX mouse with neuroblastoma (MYCN amplified).	unspecified	96
EGAD50000001514	Single-cell G&T seq from an untreated PDX mouse with neuroblastoma (MYCN amplified).	unspecified	96
EGAD50000001515	The SHH medulloblastoma tumor 7316-178 was received through the Childhood Brain Tumor Network (CBTN). From the patient tumor, disassociated cryopreserved cells stored in 10% DMSO/FBS were used. At least 50 mg of tissue (1 M cells) was used for both samples. Disassociated cells were prepared for Single Cell Multiome ATAC + Gene Expression sequencing (10× Genomics) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq S4 200 to a depth of at least 250 M reads for snATAC-seq and 200 M reads for snRNA-seq.	Illumina NovaSeq 6000	30