{"database": "metadata", "table": "run_metadata", "rows": [[70432, "SRR19831099", "SRX15874807", "SRS13564513", "SRP383398", "PRJNA851939", "Danio rerio breed:Wild type Transcriptome or Gene expression", "PRJNA851939", "Other", "Evaluation of gene expression changes in zebrafish liver following a full life cycle exposure to metformin in order to evaluate the main pathways affected", null, null, null, "M3FL", "M3FL", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:Adult|sex:female|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "M3 female", "Dre M3 female", "Dre M3 female", "Briefly  one RNA pool of 5 livers n=1  from each treatment and sex  with a minimum concentration of 40 ng/L  were subjected to a quality control  to determine RNA purity by measuring the ratio of absorbance at 260/280 nm on a NanoDrop Thermo Fisher Scientiphic  USA;  integrity  and concentration were estimated using the Agilent 2100 BioAnalizer Agilent Technologies  USA and integrity was further confirmed by 1 % agarose gel eletrophoresis. RNA samples with a RIN RNA integrity number above 6.3 passed the quality control and were used for library construction and further sequencing. post quality control proceedings  RNA samples were then enriched using oligodT beads and rRNA was removed from total RNA using the Ribo Zero Kit Illumina  USA. Subsequently  sequencing libraries were prepared using Novogene NGS RNA Library Prep Set. Briefly  Isolated mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesis was performed using mRNA template and random hexamer primers for the first strand  post which a custom second strand synthesis buffer Illumina  USA  as well as dNTPs  RNAse H and DNA polymerase I were added to start the second strand synthesis.. post end repair   A tailing   and sequencing adapter ligation  were performed. In order to select cDNA fragments of approximately 250 300 bp  samples were sonicated and magnetic beads were used to select the target fragment size  post which UTP containing second strand were removed through enzyme digestion. cDNA library was then completed  through size selection andPCR amplification.  post cDNA library completion  a preliminary quantification was performed using a Qubit 2.0 fluorometer Termo Fisher Scientific  USA  followed by Agilent 2100 Bioanalyzer to test insert size  and lastly a Q PCR to quantify the library effective concentration precisely. Quantified libraries  from each treatment and sex  were then independently subjected to sequencing Illumina Novaseq 6000 paired end 2x150  generating an average of 35 million pair end reads for each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP383398", null, null, "M3FL_1.fq.gz M3FL_2.fq.gz", "fastq fastq", 11853885000.0, 39512950.0, "M3FL 1.fq.gz", "0:150 1:150", "A:3129583480;C:2788314875;G:2819899471;T:3116000527;N:86647", 150, 150, null, null, 3129583480, 2788314875, 2819899471, 3116000527, 86647, "SRX15874807", "SRS13564513", "SRA1442579", "CIIMAR - Interdisciplinary Centre of Marine and Environmental Research|EDEC - Endocrine Disruptors and Emergent Contamina", "CIIMAR - Interdisciplinary Centre of Marine and Environmental Research", 2, 0.96636, 0.96644, 0.02786, 0.02873, 0.84954, 0.84991, 0.21022, 0.20905, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "Portugal", "2022-06-24", "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": ["70432"], "units": {}, "query_ms": 11.869580994243734}