{"database": "metadata", "table": "run_metadata", "rows": [[46225, "SRR6507308", "SRX3595750", "SRS2864123", "SRP131267", "PRJNA431425", "tp53 deficiency causes a wide tumor spectrum and elevates embryonal rhabdomyosarcoma metastasis in zebrafish", "GSE109581", "Transcriptome Analysis", "We generated tp53 deletion mutant zebrafish that spontaneously develop malignant peripheral nerve sheath tumors  angiosarcomas  germ cell tumors  and an aggressive Natural Killer cell leukemia not previously reported in zebrafish. Each tumor type efficiently engrafted into syngeneic recipient zebrafish and shared gene expression signatures with predicted cells of origin. Overall design: We generated a complete null tp53 deletion allele in syngeneic CG1 strain zebrafish using TALEN endonucleases. The list of tumors spontaneously developed in these tp53del/del animals included malignant peripheral nerve sheath tumors MPNSTs  angiosarcomas  germ cell tumors  and Natural Killer cell leukemia. We obtained 3 MPNSTs samples MPNST 1  MPNST 2 and MPNST 3  2 angiosarcoma samples Angiosarcoma 1 and Angiosarcoma 2  3 leukemia samples Leukemia 1  Leukemia 2 and Leukemia 3  and 1 sample of germ cell tumor GermCell 1. We also assessed the role of tp53 in kRASG12D induced human embryonal rhabdomyosarcoma ERMS using large scale cell transplantation assays and live fluorescent imaging over time. We obtained 3 ERMS samples ERMS 1  ERMS 2 and ERMS 3. All these tumor samples were compared to 3 background CG1 samples samples WholeFish 1  WholeFish 2 and WholeFish 3.", null, "pubmed:30192230", null, "MPNST 1", "GSM2946789", null, "tissue:malignant peripheral nerve sheath tumor|genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant  dissection", "MPNST 1", "Reads were aligned with STAR v2.4.0; PCR duplicates were removed with Picard v1.95 and reads aligning to ribosomal RNA were removed with RSeQC; gene counts were obtained from reads with an alignment quality of at least 10 using featureCounts and transformed to transcript per million TPM units. Genome build: GRCz10 Supplementary files format and content: Counts matrix provided as supplementary file.", "malignant peripheral nerve sheath tumor", "Tissue was harvested using 90% PBS + 5% FBS. FACS sorting was performed to obtain tumor cell fraction with 85% purity and 90% viability.", "Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit", "Animals were raised at 28 degrees celcius", "genotype:CG1 tp53 homozygous mutant|tumor type:spontaneous|procedure:primary transplant  dissection", "GSM2946789", "GSM2946789: MPNST 1; Danio rerio; RNA Seq", "GSM2946789", null, "1", "Total RNA was extracted using RLT buffer Qiagen and purified using RNeasy kit Qiagen as per manufacturer instructions Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit", "GEO Accession:GSM2946789", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP131267", null, null, "MPNST_1.bam", "bam", 4758494608.0, 23556904.0, "GSM2946789 r1", "0:101 1:101", "A:1256101624;C:1121363306;G:1131796356;T:1248769939;N:463383", 101, 101, null, null, 1256101624, 1121363306, 1131796356, 1248769939, 463383, "SRX3595750", "SRS2864123", "SRA652013", "GEO", "Pathology, Massachusetts General Hospital", 2, 0.94674, 0.9501, 0.07974, 0.07759, 0.70761, 0.71155, 0.48864, 0.49029, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-01-24", "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": ["46225"], "units": {}, "query_ms": 8.876722000422888}