{"database": "metadata", "table": "run_metadata", "rows": [[52299, "SRR9159932", "SRX5933017", "SRS4846224", "SRP199854", "PRJNA543743", "A temporal map of gene expression pattern during zebrafish liver regeneration.", "PRJNA543743", "Whole Genome Sequencing", "Zebrafish is increasingly being used to study liver injury and regeneration. However  very little is known about molecular players that respond to injury and those important for liver regeneration. We use a metronidazole nitroreductase MTZ nfsb based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Here  we generate a comprehensive temporal map of gene expression changes during regeneration through RNA sequencing of liver samples at various stages of injury and regeneration. Analysing this data  we find that xxx post injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole induced ROS by activating oxido reductase pathways and apoptosis machinery. xxx post injury  liver cells down regulate many functional genes including complement protein synthesis  bile acid and lipid biosynthesis  in a concerted manner. At 6 xxx post injury  we find a dramatic induction of cholesterol biosynthesis and protein folding machinery  with expression levels returning to pre damage levels by 8 days  suggesting an important role for these pathways in liver regeneration. This chronological transcriptomic map of liver regeneration in zebrafish would serve as a framework for further studies in understanding  and for screening for compounds that augment liver regeneration.", null, null, null, null, "t0 rep1", null, "strain:Transgenic|age:1year|dev stage:adult|sex:female|tissue:liver|disease stg:untreated|Replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "t0 rep1", "t0 rep1", "t0 rep1", "Random PCR", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP199854", null, null, "Untreated_Rep1_R1.fastq.gz Untreated_Rep1_R2.fastq.gz", "fastq fastq", 15183490000.0, 54226750.0, "Untreated Rep1 R1.fastq.gz", "0:140 1:140", "A:3868549452;C:3725214028;G:3555537015;T:3992531756;N:41657749", 140, 140, null, null, 3868549452, 3725214028, 3555537015, 3992531756, 41657749, "SRX5933017", "SRS4846224", "SRA891455", "CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.92869, 0.82319, 0.15668, 0.1344, 0.80052, 0.81067, 0.44034, 0.43611, 140, 140, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-05-30", "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": ["52299"], "units": {}, "query_ms": 7.493735000025481}