run_metadata: 44960

This data as json

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44960	SRR6334486	SRX3433614	SRS2724932	SRP125946	PRJNA420576	c MYC drives a subset of high risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification [RNA seq]	GSE107518	Transcriptome Analysis	Childhood neuroblastoma is known for MYCN gene amplification and here we show that in a separate subset of cases MYC itself is activated due to enhancer hijacking from chromosomal translocations or duplications thus defining a unique subset of high risk disease. Overall design: RNA seq in zebrafish overexpressing human c Myc or n Myc	parent bioproject:PRJNA398387	pubmed:29284669		cMYCoe line2 r3	GSM2870453		tissue:Neuroblastoma tumor cells\|cell type:EGFP+ transformed neuroblasts\|overexpression:c Myc	cMYCoe line2 r3	Reads were aligned to a custom version of the zebrafish reference genome containing danRer10 references for all zebrafish chromosomes and "pseudochromosomes" created from the coding sequence of human c Myc and n Myc used in the experimental system Reads were aligned using tophat with parameters no novel juncs and in single end mode Read counts per RefSeq gene and human c Myc and n Myc were quantified using htseq count using parameters stranded=no i gene name f bam Reads per kilobase of exon per million mapped reads were created from these readcounts by dividing by the number of kilobases in all isoforms with the same gene name and then by the millions of mapped reads Supplementary files format and content: WIG filess represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads per million and floored at 0.1	Neuroblastoma tumor cells		Sorted EGFP+ cells were sorted then total RNA was extracted with Trizol LS. Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit Clontech. Enriched mRNA was then applied to library preparation according to manufacturer’s protocol NEBNext Ultra. post repeated quality control for average DNA input size of 300 bp the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired end reads.	EGFP+ neuroblastoma cells were harvested from tumor bearing MYCN and MYC transgenic zebrafish. Tumors were mechanically homogenized and EGFP+ cells were sorted directly into Trizol LS	cell type:EGFP+ transformed neuroblasts\|overexpression:c Myc	GSM2870453	GSM2870453: cMYCoe line2 r3; Danio rerio; RNA Seq	GSM2870453		1	Sorted EGFP+ cells were sorted then total RNA was extracted with Trizol LS. Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit Clontech. Enriched mRNA was then applied to library preparation according to manufacturer's protocol NEBNext Ultra. post repeated quality control for average DNA input size of 300 bp the samples were sequenced on a HiSeq Illumina sequencer with 2x100bp paired end reads.	GEO Accession:GSM2870453	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP125946			cMYCoe_line2_r3.20161116_MYC-7_MWZ3676_S7_R1_001.fastq.gz cMYCoe_line2_r3.20161116_MYC-7_MWZ3676_S7_R2_001.fastq.gz	fastq fastq	9707643300.0	64717622.0	GSM2870453 r1	0:75 1:75	A:2656490466;C:2245711917;G:2271269818;T:2529962783;N:4208316	75	75			2656490466	2245711917	2271269818	2529962783	4208316	SRX3433614	SRS2724932	SRA634977	GEO	Young Lab, Whitehead Institute for Biomedical Research	2	0.89705	0.89958	0.06199	0.06253	0.75706	0.76232	0.54548	0.53954	75	75	B	B	biological fallback assumption	illumina	nextseq	full_length	rrna_depletion	nebnext	bulk	unknown	unknown		United States	2017-11-29	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor