run_metadata: 34095

This data as json

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
34095	SRR31050910	SRX26435350	SRS22952030	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		pubmed:39556913		Zebrafish Testicle Plastic Replicate 3 Animal 1	GSM8583343		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 1	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	GSM8583343	GSM8583343: Zebrafish Testicle Plastic Replicate 3 Animal 1; Danio rerio; RNA Seq	GSM8583343 r1	GSM8583343	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP539687			M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_1.fq M6_C2_R3_A1_EKRN230074902-1A_HWT7HDSX7_L3_2.fq	fastq fastq	21334650000.0	71115500.0	GSM8583343 r1												SRX26435350	SRS22952030	SRA1994234	UAB (Universidad Autónoma de Barcelona)	UAB (Universidad Autónoma de Barcelona)												B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	bulk	bulk		Spain	2024-10-20	Adult	Adult	Gonad	Reproductive System