{"database": "metadata", "table": "run_metadata", "rows": [[34489, "SRR31790710", "SRX27151925", "SRS23606410", "SRP552945", "PRJNA1201093", "Fine particulate matter PM2.5 induces microRNA 192\u20135p causing glomerular damage", "GSE285038", "Transcriptome Analysis", "To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5\u00b0C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 \u00d7 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep\u2122 RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.", null, "pubmed:40373708", null, "RNA zebrafish larvae control rep 2", "GSM8695644", null, "source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing", "RNA zebrafish larvae control rep 2", "RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample", "larvea", null, "RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer\u00b4s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.", null, "tissue:larvea|treatment:control", "GSM8695644", "GSM8695644: RNA zebrafish larvae control rep 2; Danio rerio; RNA Seq", "GSM8695644 r1", "GSM8695644", "1", "RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer\u00b4s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP552945", null, null, "RNA_zebrafish_larvae_control_rep_2_R1.fq.gz RNA_zebrafish_larvae_control_rep_2_R2.fq.gz", "fastq fastq", 6347285700.0, 21157619.0, "GSM8695644 r1", "0:150 1:150", "A:1687168204;C:1494146408;G:1490096893;T:1672074832;N:3799363", 150, 150, null, null, 1687168204, 1494146408, 1490096893, 1672074832, 3799363, "SRX27151925", "SRS23606410", "SRA2123535", "Institute for Stem Cell Biology, RWTH Aachen University Medical School", "Institute for Stem Cell Biology, RWTH Aachen University Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "bulk", "bulk", null, "Germany", "2024-12-20", "Larval", "Larval", "Undetermined", "Undetermined"]], "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": ["34489"], "units": {}, "query_ms": 7.240127000841312}