{"database": "metadata", "table": "run_metadata", "rows": [[40953, "SRR3465550", "SRX1735452", "SRS1416505", "SRP074122", "PRJNA319956", "Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.", "GSE80768", "Transcriptome Analysis", "Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.", null, "pubmed:27783941", null, "9267X5 tumor", "GSM2136818", null, "source name:brain tumor|tissue:brain tumor", "9267X5 tumor", "USeq\u2019s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign  allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq\u2019s SamTranscriptomeParser application  which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq\u2019s DefinedRegionDifferentialSeq application  which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts  FPKM values  log2FC and FDR values", "brain tumor", "Normal brain and brain tumors were dissected from zebrafish  briefly submerged in RNAlater  snap frozen in liquid nitrogen  and stored at  80C. To extract RNA  samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.", "tissue:brain tumor", "GSM2136818", "GSM2136818: 9267X5 tumor; Danio rerio; RNA Seq", "GSM2136818", null, "1", "Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.", "GEO Accession:GSM2136818", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP074122", null, null, "9267X5_120613_SN141_0510_AC0TF4ACXX_7.txt.gz", "fastq", 1030064550.0, 20601291.0, "GSM2136818 r1", "0:50", "A:275570887;C:242993408;G:235025540;T:276437064;N:37651", 50, null, null, null, 275570887, 242993408, 235025540, 276437064, 37651, "SRX1735452", "SRS1416505", "SRA421168", "GEO", "Oncological Sciences, University of Utah", 1, 0.91852, null, 0.0986, null, 0.70451, null, 0.47961, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-28", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"]], "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": ["40953"], "units": {}, "query_ms": 11.740686997654848}