{"database": "metadata", "table": "run_metadata", "rows": [[32629, "SRR29382473", "SRX24896629", "SRS21602926", "SRP513565", "PRJNA1123307", "To identify differentially expressed genes in ventricular tissue between wildtype control and the 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish at six months.", "GSE269725", "Transcriptome Analysis", "To seek molecular mechanisms underlying the mechanisms of mutant genotypes by comparing them witht he wild types  we performed whole transcriptome RNA sequencing experiments using ventricular tissue isolated from 6 mpf mtorxu015/+ mutant  Tgcmlc2:tfeb transgenic zebrafish and corresponding WT siblings. Overall design: Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings.", null, null, null, "tg3", "GSM8325761", null, "source name:Heart|tissue:Heart|genotype:Tgcmlc2:tfeb transgenic|geo loc name:missing|collection date:missing", "tg3", "Image analysis and base calling were conducted by the HiSeq Control Software HCS. Raw sequence data .bcl files generated from Illumina HiSeq was converted into fastq files and de multiplexed using Illumina's bcl2fastq 2.17 software. Sequence read will be trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads will be mapped to the ZV9 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Assembly: Danio rerio.GRCz11.cdna.all.fa Supplementary files format and content: merged gene counts.txt", "Heart", null, "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "tissue:Heart|genotype:Tgcmlc2:tfeb transgenic", "GSM8325761", "GSM8325761: tg3; Danio rerio; RNA Seq", "GSM8325761 r1", "GSM8325761", "1", "Total RNA was extracted from dissected ventricular tissue of 6 mpfmtorxu015/+ mutant  Tgcmlc2:tfeb transgenic and corresponding  WT siblings. Five ventricles were pooled as one sample and three biological replicates for each genotype were sequenced using the HiSeq 2000 platform. Illumina with a 50 bp paired end sequencing protocol in the Mayo Clinic DNA Sequencing Core Facility", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP513565", null, null, "tgTFEB-3.FCC83VDACXX_L2_R2_IACTTGA.fastq.gz tgTFEB-3.FCC83VDACXX_L2_R1_IACTTGA.fastq.gz", "fastq fastq", 4329815748.0, 42449174.0, "GSM8325761 r1", "0:51 1:51", "A:1142130932;C:1032964058;G:1007903605;T:1146154372;N:662781", 51, 51, null, null, 1142130932, 1032964058, 1007903605, 1146154372, 662781, "SRX24896629", "SRS21602926", "SRA1897306", "University of Maryland", "University of Maryland", 2, 0.93676, 0.93675, 0.07682, 0.07757, 0.77027, 0.77293, 0.50098, 0.5234, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-06-12", "Adult", "Adult", "Heart", "Cardiovascular 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": ["32629"], "units": {}, "query_ms": 7.2931400063680485}