{"database": "metadata", "table": "run_metadata", "rows": [[40028, "SRR2751017", "SRX1362087", "SRS1125440", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 109", "GSM1915523", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 109", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915523", "GSM1915523: NH FLI liver 109; Danio rerio; RNA Seq", "GSM1915523", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR109.fq.gz", "fastq", 2349260700.0, 46985214.0, "GSM1915523 r1", "0:50", "A:619110926;C:556823390;G:547569893;T:625605583;N:150908", 50, null, null, null, 619110926, 556823390, 547569893, 625605583, 150908, "SRX1362087", "SRS1125440", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94144, null, 0.06318, null, 0.76282, null, 0.57815, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "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": ["40028"], "units": {}, "query_ms": 10.11915799608687}