{"database": "metadata", "table": "run_metadata", "rows": [[34094, "SRR31050909", "SRX26435351", "SRS22952031", "SRP539687", "PRJNA1175381", "Short term polystyrene nanoplastic exposure alters zebrafish male and female germline and reproductive outcomes  unveiling pollutant impacted molecular pathways", "GSE279916", "Transcriptome Analysis", "Nanoplastics pollution is a rising environmental concern whose impacts on biodiversity and human health are far from being understood. This is particularly salient in aquatic ecosystems  where the majority of species depend on external fertilization for reproduction. Here we evaluated the effects of a short term exposure to engineered polystyrene nanoplastics NPs in the zebrafish germ line to further explore their impact on reproduction. To this end  zebrafish Danio rerio were exposed to 5 mg/L of 45 nm polystyrene PS NPs via water for 96h. We show that  in males  nanoplastics induced testicular histological alterations with abnormal sperm clustering and chromatin compaction  resulting in viable spermatozoa but with reduced motility. Moreover  in females we observed an alteration in oocyte stages frequencies during oogenesis  possibly reflecting alterations in oocyte growth. RNA sequencing analysis in male testis links nanoplastic induced alterations in the expression of genes involved in chromatin structure  meiosis and DNA double strand break formation and repair progression  and gametes recognition. Flow cytometry analysis revealed that the observed effects in males were directly due to nanoplastics penetrating the testicular barrier and being internalized within germline cells. Overall  our results demonstrate that acute exposure to NPs can compromise reproductive fitness  underscoring the environmental and health impacts of NPs pollution. Overall design: Bulk RNA seq from adult testis from control 3 samples and treated animals 3 samples", null, "pubmed:39556913", null, "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "GSM8583344", null, "source name:testicles|tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic|geo loc name:missing|collection date:missing", "Zebrafish  Testicle  Plastic  Replicate 3  Animal 3", "Anaconda The sequencing quality was checked before performing the assembly. STAR bioconda was used for the assembly smartools bioconda was used to generate the intermediate files Sam and Bam Counts were obtained from the bam intermediate file Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample", "testicles", "Half of the fish were exposed to polystyrene nanoplastics each 24 hours added in the water during 96 hours accute exposure. The rest were used as controls  so no plastics were added in the water.", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", "Adult zebrafish were maintained at the animal house under standard conditions", "tissue:testicles|cell line:germline|genotype:WT|treatment:Plastic", "GSM8583344", "GSM8583344: Zebrafish  Testicle  Plastic  Replicate 3  Animal 3; Danio rerio; RNA Seq", "GSM8583344 r1", "GSM8583344", "1", "Snap frozen samples were homogenized in Trizol. Chloroform was added to separate RNA and isopropanol was used to precipitate. post ethanol washing  samples were send to Novogene for library contruction and sequencing. By manufacturer Novogene  using poly A enrichment", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP539687", null, null, "M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A3_EKRN230074904-1A_HWT7HDSX7_L3_2.fq", "fastq fastq", 24813339000.0, 82711130.0, "GSM8583344 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26435351", "SRS22952031", "SRA1994234", "UAB (Universidad Aut\u00f3noma de Barcelona)", "UAB (Universidad Aut\u00f3noma de Barcelona)", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Spain", "2024-10-20", "Adult", "Adult", "Gonad", "Reproductive 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": ["34094"], "units": {}, "query_ms": 8.633801000542007}