run_metadata: 42485

This data as json

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42485	SRR5639263	SRX2877663	SRS2249439	SRP108529	PRJNA388953	c MYC drives neuroblastoma tumorigenesis and retinoic acid resistance in zebrafish [RNA Seq]	GSE99567	Transcriptome Analysis	Neuroblastoma is an often intractable tumor that accounts for 15% of childhood cancer deaths. In addition to MYCN amplification in 20% of tumors 11% express high levels of c MYC MYC protein. To study this newly defined subgroup we have created a novel transgenic zebrafish model in which overexpression of MYC in the peripheral sympathetic nervous system drives early onset neuroblastoma. Overall design: RNA seq was performed on MYC and MYCN driven neuroblastoma tumors to determine chromatin accesibility in these cells	parent bioproject:PRJNA388873			MYC 3	GSM2646584		tissue:EGFP+ neuroblastoma cells were harvested from tumor bearing MYC transgenic zebrafish.\|cell type:EGFP+ neuroblasts	MYC 3	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to dr7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: dr7 Supplementary files format and content: excel files include RPKM values for each Sample ...	EGFP+ neuroblastoma cells were harvested from tumor bearing MYC transgenic zebrafish.		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+ neuroblasts	GSM2646584	GSM2646584: MYC 3; Danio rerio; RNA Seq	GSM2646584		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:GSM2646584	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP108529			20161116_MYC-3_MWZ3676_S3_R1_001.fastq.gz 20161116_MYC-3_MWZ3676_S3_R2_001.fastq.gz	fastq fastq	9499251600.0	63328344.0	GSM2646584 r1	0:75 1:75	A:2600983566;C:2193461949;G:2224307535;T:2476379293;N:4119257	75	75			2600983566	2193461949	2224307535	2476379293	4119257	SRX2877663	SRS2249439	SRA569347	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.9202	0.92206	0.07816	0.07901	0.74612	0.75268	0.55199	0.54541	75	75	B	B	biological fallback assumption	illumina	hiseq_era	full_length	rrna_depletion	nebnext	bulk	unknown	unknown		United States	2017-06-01	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor