{"database": "metadata", "table": "run_metadata", "rows": [[36511, "SRR566691", "SRX185756", "SRS361909", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M+D ", "GSM1000556: M+D  1", "GSM1000556", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D  1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000556", "GSM1000556: M+D  1; Danio rerio; RNA Seq", "GSM1000556 1", null, "1", null, "GEO Accession:GSM1000556", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_1_QV.qual M+D-_1.csfasta", "SOLiD_native SOLiD_native", 1286706820.0, 36763052.0, "GSM1000556 r1", "0:35", "0:252864341;1:338709089;2:436928155;3:256235022;.:1970213", 35, null, null, null, null, null, null, null, null, "SRX185756", "SRS361909", "SRA058618", "GEO", "National University of Singapore", 1, 0.12399, null, 0.00617, null, 0.98752, null, 0.50351, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary 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": ["36511"], "units": {}, "query_ms": 11.65183800185332}