{"database": "metadata", "table": "run_metadata", "rows": [[40457, "SRR3169300", "SRX1584901", "SRS1302560", "SRP070127", "PRJNA312107", "SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [RNA Seq]", "GSE77922", "Transcriptome Analysis", "We report gene expression data for zebrafish melanomas overexpressing human SATB2 and EGFP. Overall design: RNA seq was performed on three biological replicates of primary zebrafish melanoma tumors that were excized from MCR:EGFP control and MCR:SATB2 overexpressing TgBRAF V600E;p53 / ; mitf /  zebrafish.", "parent bioproject:PRJNA312106", null, null, "MCR:SATB2 tumor 2", "GSM2061398", null, "source name:SATB2 2|tissue:primary melanoma tumor|genotype:Tgmitfa:BRAFV600E; p53 / ; mitfa / ", "MCR:SATB2 tumor 2", "Quality control of RNA Seq datasets was performed by FastQC18 and Cutadapt19 to remove adaptor sequences and low quality regions. The high quality reads were aligned to UCSC build danRer7 of zebrafish genome using Tophat20 2.0.11 without xxx splicing form calls. Transcript abundance and differential expression were calculated with Cufflinks21 2.2.1. FPKM values were used to normalize and quantify each transcript. Genome build: Danio rerio UCSC danRer7 Supplementary files format and content: tab delimited text file containg the FPKM value of each gene", "SATB2 2", "Zebrafish Tgmitfa:BRAFV600E; p53 / ; mitfa /  one cell stage embryos were injected with a MiniCoopR expression vector to induce melanocyte specific overexpression of either EGFP control or human SATB2  raised to maturity and monitored for melanoma formation.", "Zebrafish melanomas were isolated and mechanically homogenized in RTL buffer Qiagen containing \u03b2 mercaptoethanol. Tumor lysates were transferred onto a QiaShredder column Qiagen  and RNA isolation was performed using the RNA Micro Plus kit Qiagen according to the manufacturers instruction. Total RNA was depleted of ribosomal RNA with the Ribo Zero Gold kit Epicentre. Ribosome depleted RNA was used to create multiplexed RNA seq libraries NEBNext Ultra  according to manufacturer's protocol", null, "tissue:primary melanoma tumor|genotype:Tgmitfa:BRAFV600E; p53 / ; mitfa / ", "GSM2061398", "GSM2061398: MCR:SATB2 tumor 2; Danio rerio; RNA Seq", "GSM2061398", null, "1", "Zebrafish melanomas were isolated and mechanically homogenized in RTL buffer Qiagen containing \u03b2 mercaptoethanol. Tumor lysates were transferred onto a QiaShredder column Qiagen  and RNA isolation was performed using the RNA Micro Plus kit Qiagen according to the manufacturers instruction. Total RNA was depleted of ribosomal RNA with the Ribo Zero Gold kit Epicentre. Ribosome depleted RNA was used to create multiplexed RNA seq libraries NEBNext Ultra  according to manufacturer's protocol", "GEO Accession:GSM2061398", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP070127", null, null, "EvR-6_R1.fastq.gz EvR-6_R2.fastq.gz", "fastq fastq", 8239248720.0, 40788360.0, "GSM2061398 r1", "0:101 1:101", "A:2050158124;C:2039805258;G:2055117618;T:2091456014;N:2711706", 101, 101, null, null, 2050158124, 2039805258, 2055117618, 2091456014, 2711706, "SRX1584901", "SRS1302560", "SRA353730", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.89794, 0.89327, 0.4125, 0.40937, 0.74, 0.74598, 0.49301, 0.51668, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-02-15", "Undetermined", "Embryo", "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": ["40457"], "units": {}, "query_ms": 9.81924899679143}