{"database": "metadata", "table": "run_metadata", "rows": [[31482, "SRR28362831", "SRX23967976", "SRS20767207", "SRP495638", "PRJNA1088730", "Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress", "PRJNA1088730", "Other", "Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand  ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer  deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study  the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.", null, null, null, "noxo1a re#2", "noxo1a re#2", null, "strain:AB strain|dev stage:Larvae|collection date:2023 03 05|geo loc name:China: Wuhan|sex:not determined|tissue:Whole body|genotype:noxo1a mutant with indel|treatment:Exposed to 10 \u00b0C for 12 h followed by recovery at 28 \u00b0C for 6 h|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "noxo1a re#2", "noxo1a re#2", "noxo1a re#2", "One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion  Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then  the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation  first and second strand cDNA synthesis  double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally  the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California  San Francisco using Hiseq 3000.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495638", null, null, "noxo1a-re-2_S1_L004_R1_001.fastq.gz noxo1a-re-2_S1_L004_R2_001.fastq.gz", "fastq fastq", 6021534600.0, 20071782.0, "noxo1a re 2 S1 L004 R1 001.fastq.gz", "0:150 1:150", "A:1597183597;C:1408878472;G:1434927510;T:1580500451;N:44570", 150, 150, null, null, 1597183597, 1408878472, 1434927510, 1580500451, 44570, "SRX23967976", "SRS20767207", "SRA1825819", "Chinese Academy of Sciences|Institute of Hydrobiology", "Chinese Academy of Sciences", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "China", "2024-03-16", "Larval", "Larval", "Trunk", "Surface Structure"]], "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": ["31482"], "units": {}, "query_ms": 13.606666005216539}