{"database": "metadata", "table": "run_metadata", "rows": [[47718, "SRR6841473", "SRX3797301", "SRS3049359", "SRP135774", "PRJNA438478", "RNAseq of wild type zebrafish germline ovary  oocyte  testis", "GSE111882", "Transcriptome Analysis", "Goal of this study is the gene expression analysis of the zebrafish adult germline ovary  oocyte  testis Overall design: Three tissue types ovary  oocyte  testis from adult wildtype TLAB zebrafish; two replicates each", null, "pubmed:30190407;pubmed:34556579", null, "testis rep2", "GSM3043290", null, "source name:whole wildtype zebrafish testis dissected from male|tissue:testis|genotype:wild type|strain:TLAB", "testis rep2", "Libraries were sequenced on a HiSeq 2000 paired end 76 bp reads. Reads were aligned to GRCz10  using the Ensembl transcriptome release 88. A custom file was generated by adding bouncer based on its position coordinates tracking ID: bouncer; exon = Chr18:50858259 50858859   strand; CDS = chr18:50858285 50858663    strand. The following command was used to map each sample: \u2018tophat   o <output directory>  p 16\u00a0  library type fr firststrand \u2013no novel juncs\u00a0\u2013g 1\u00a0\u2013G <Custom gene table> <Bowtie2 genome index> <fastq reads>\u201d.\u00a0 Quantification of transcript levels FPKM was determined using cuffnorm\u00a0with the following command \u201ccuffnorm  p 22   library type=fr firststrand  L < labels >  o <output directory> <Custom gene table> <aligned reads.bam file>. Genome build: GRCz10 Supplementary files format and content: tab delimited text file containing FPKMs", "whole wildtype zebrafish testis dissected from male", null, "Total RNA was isolated using the standard TRIzol Invitrogen protocol  and genomic DNA was removed by TURBO DNase treatment followed by phenol/chloroform extraction. Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 Strand specific libraries for 76 bp paired end sequencing were prepared from cDNA by the Broad Institute Sequencing Platform.", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle until point of sample collection.", "tissue:testis|genotype:wild type|strain:TLAB", "GSM3043290", "GSM3043290: testis rep2; Danio rerio; RNA Seq", "GSM3043290", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol  and genomic DNA was removed by TURBO DNase treatment followed by phenol/chloroform extraction. Libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 Strand specific libraries for 76 bp paired end sequencing were prepared from cDNA by the Broad Institute Sequencing Platform.", "GEO Accession:GSM3043290", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP135774", null, null, "zf_testis_2_6_R.fq.gz zf_testis_2_6_F.fq.gz", "fastq fastq", 4863124784.0, 31994242.0, "GSM3043290 r2", "0:76 1:76", "A:1239366804;C:1186097287;G:1202405036;T:1232271257;N:2984400", 76, 76, null, null, 1239366804, 1186097287, 1202405036, 1232271257, 2984400, "SRX3797301", "SRS3049359", "SRA666799", "GEO", "IMP", 2, 0.94462, 0.95606, 0.13046, 0.13473, 0.73551, 0.74063, 0.50501, 0.50288, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Austria", "2018-03-15", "Undetermined", "Undetermined", "Gonad", "Reproductive 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": ["47718"], "units": {}, "query_ms": 11.416205001296476}