{"database": "metadata", "table": "run_metadata", "rows": [[75651, "SRR24755924", "SRX20532024", "SRS17840667", "SRP439951", "PRJNA977045", "Microbiota dysbiosis associated with type 2 diabetes like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]", "GSE233631", "Transcriptome Analysis", "Mixtures of chlorinated persistent organic pollutants C POPs Mix are chemically related risk factors for type 2 diabetes mellitus T2DM; however  the effects of chronic exposure to C POPs Mix on microbial dysbiosis remain poorly understood. Herein  male and female zebrafish were exposed to C POPs Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02  0.1  and 0.5 \u00b5g/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance  richness  and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C POPs Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 \u00b5g/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis  Rhizobium tibeticum  Bifidobacterium catenulatum  B. adolescentis  and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation  which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM related molecular pathways. Thus  microbial dysbiosis in T2DM triggered zebrafish occurred as a result of chronic exposure to C POPs Mix  indicating strong host\u2013microbiome interactions. Overall design: Samples consisted of the control group and three treatment groups exposed to 0.02  0.1  and 0.5 ug/L of C POPs Mix containing five OCPs and Aroclor1254 for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C POPs Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA seq on the Illumina HiSeq 2500 platform. For 16S rRNA seq analysis  total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.", "parent bioproject:PRJNA977043", null, null, "Control 0", "GSM7431679", null, "source name:Liver|tissue:Liver|Sex:female|treatment:DMSO|genotype:WT|time:84 days|geo loc name:missing|collection date:missing", "Control 0", "Quality trimming was performed using FastQC v0.11.9 Quality based trimming was performed using cutadapt v2.8 Alignment was performed using STAR v2.7.1a Gene counts were performed with RSEM v1.3.3  featureCounts v2.0.0  HTSeq count v0.11.2  and Cufflinks v2.2.1 Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1 Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2 Supplementary files format and content: FPKM count table is a CSV format.", "Liver", "A total of 360 zebrafish including 180 females and 180 males were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02  0.1  0.5 \u03bcg/L C POPs Mix for 12 weeks in an automatic flow through exposure system TOX MIXII  Hanalab  Daejeon  South Korea.", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", "Zebrafish Danio rerio  wild type AB strain aged 10\u201312 month were maintained in a flow through system Tecniplast  Buguggiate  Italy with a 14 h light/10 h dark photoperiod at a temperature of 28.5\u00b0C \u00b1 0.5\u00b0C and pH of 7.0\u20137.5. The zebrafish were fed thrice daily with Gemma micro 300 Skretting  West brook  Maine  USA.", "tissue:Liver|Sex:Female|treatment:DMSO|genotype:WT|time:84 days", "GSM7431679", "GSM7431679: Control 0; Danio rerio; RNA Seq", "GSM7431679 r1", "GSM7431679", "1", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP439951", null, null, "Control_1.fq.gz Control_2.fq.gz", "fastq fastq", 7663427274.0, 25375587.0, "GSM7431679 r1", "0:151 1:151", "A:2102047070;C:1720814862;G:1775607282;T:2064903634;N:54426", 151, 151, null, null, 2102047070, 1720814862, 1775607282, 2064903634, 54426, "SRX20532024", "SRS17840667", "SRA1645529", "Biology, University of Ottawa", "Biology, University of Ottawa", 2, 0.959, 0.89994, 0.04409, 0.04019, 0.84502, 0.84983, 0.30528, 0.30485, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2023-05-28", "Multi-stage", "Multi-stage", "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": ["75651"], "units": {}, "query_ms": 14.552496002579574}