{"database": "metadata", "table": "run_metadata", "rows": [[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.", null, "pubmed:33602789", null, "MYCN only 1", "GSM3768992", null, "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", null, "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\u2019s instructions. RNA integrity RIN was verified on an Agilent 2100 bioanalyzer Agilent Technologies  Santa Clara  CA  USA and 100 200 ng of RNA RIN \u2265 7.0 in a 5 \u03bcl 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.", null, "tissue:peripheral sympathetic nervous system|genotype:MYCN overexpression only", "GSM3768992", "GSM3768992: MYCN only 1; Danio rerio; RNA Seq", "GSM3768992", null, "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 \u2265 7.0 in a 5 \u03bcl 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", null, "SRP198600", null, null, "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, null, null, 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", null, "United States", "2019-05-16", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["52259"], "units": {}, "query_ms": 7.770873999106698}