run_metadata: 52259

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
52259	SRR9067639	SRX5843743	SRS4768675	SRP198600	PRJNA543225	GAS7 Deficiency Promotes Metastasis of MYCN driven Neuroblastoma	GSE131307	Transcriptome Analysis	Neuroblastoma NB the most common extracranial solid tumor in children often metastasizes at a high rate. Here we demonstrate that loss of function of the growth arrest specific 7 gene GAS7 located on Chr17p13.1 a deleted region in a subset of high risk NB accelerates dissemination of MYCN overexpressing tumor cells in both zebrafish and xenografted mice models. Transcriptomic analysis of neuroblasotma tumors isolated from transgenic zebrafish overexpressing MYCN oncogene alone or MYCN with knockout of gas7 gene revealed that gene signitures affecting tumor cell cell or cell extracellular matrix interactions are significantly downregulated in tumors with gas7 loss of function. Our results provide the first genetic evidence that loss of function of a gene located in the Chr17p region contributes significantly to NB metastasis. Overall design: Examination of the transcriptomic profiles of neuroblastomas arose from transgenic fish overexpressing MYCN alone or MYCN with knockout of gas7.		pubmed:33602789		MYCN only 1	GSM3768992		source name:zebrafish tumor\|tissue:peripheral sympathetic nervous system\|genotype:MYCN overexpression only	MYCN only 1	Fastq files of pair end RNA Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC danRer10 using Bowtie2 2.2.6 with default parameters. Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages. Genome build: danRer10 Supplementary files format and content: tab delimited gene counts	zebrafish tumor		RNA was extracted from zebrafish tumors overexpressing MYCN alone or MYCN with knokcout of gas7. Total RNA was extracted using the Trizol reagent as per manufacturer’s instructions. RNA integrity RIN was verified on an Agilent 2100 bioanalyzer Agilent Technologies Santa Clara CA USA and 100 200 ng of RNA RIN ≥ 7.0 in a 5 μl volume was used for library preparation and RNA sequencing RNAseq. Paired end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit Illumina by the Mayo Clinic sequencing core facilities Rochester MN followed by quality control cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de multiplexed and converted to FASTQ format using CASAVA software from Illumina by the Mayo Clinic core.		tissue:peripheral sympathetic nervous system\|genotype:MYCN overexpression only	GSM3768992	GSM3768992: MYCN only 1; Danio rerio; RNA Seq	GSM3768992		1	RNA was extracted from zebrafish tumors overexpressing MYCN alone or MYCN with knokcout of gas7. Total RNA was extracted using the Trizol reagent as per manufacturer's instructions. RNA integrity RIN was verified on an Agilent 2100 bioanalyzer Agilent Technologies Santa Clara CA USA and 100 200 ng of RNA RIN ≥ 7.0 in a 5 μl volume was used for library preparation and RNA sequencing RNAseq. Paired end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit Illumina by the Mayo Clinic sequencing core facilities Rochester MN followed by quality control cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de multiplexed and converted to FASTQ format using CASAVA software from Illumina by the Mayo Clinic core.	GEO Accession:GSM3768992	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP198600			MYCN_only_1_R1.fastq.gz MYCN_only_1_R2.fastq.gz	fastq fastq	7805035378.0	38638789.0	GSM3768992 r1	0:101 1:101	A:1937052027;C:1952150867;G:1975095434;T:1936472131;N:4264919	101	101			1937052027	1952150867	1975095434	1936472131	4264919	SRX5843743	SRS4768675	SRA887417	GEO	Mayo Clinic	2	0.83391	0.83675	0.33943	0.33988	0.72058	0.72214	0.54093	0.53711	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2019-05-16	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor