{"database": "metadata", "table": "run_metadata", "rows": [[33165, "SRR29809737", "SRX25309006", "SRS21984114", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 4", "GSM8393513", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393513", "GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq", "GSM8393513 r1", "GSM8393513", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "30_2.fq.gz 30_1.fq.gz", "fastq fastq", 4240862400.0, 21204312.0, "GSM8393513 r1", "0:100 1:100", "A:1146088921;C:972830110;G:990127288;T:1131816081;N:0", 100, 100, null, null, 1146088921, 972830110, 990127288, 1131816081, 0, "SRX25309006", "SRS21984114", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.93888, 0.9444, 0.08826, 0.08671, 0.70431, 0.70212, 0.48083, 0.48199, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "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": ["33165"], "units": {}, "query_ms": 9.696555003756657}