run_metadata: 29579
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 |
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| 29579 | SRR27387422 | SRX23063705 | SRS20023727 | SRP480720 | PRJNA1059246 | Mixture toxicity of 6PPD quinone and polystyrene nanoplastics in zebrafish | PRJNA1059246 | Other | Tyre wear particles are the second largest source of microplastics in the ocean following abrasion of synthetic fibres. In addition to the particles themselves TWPs contain many harmful chemicals including 6PPD. This chemical reacts with atmospheric ozone and forms the toxic compound 6PPD quinone which poses a danger to aquatic life. There is a knowledge gap in understanding risks associated with thecombined toxicity of nanoplastics and 6PPDq. The present study aimed to investigate the toxicity of NPs and 6PPDq on adult zebrafish. However we found significant hyperlocomotion in zebrafish exposed to 6PPDq and this effect was even more substantial post co exposure with PSNPs. The more pronounced toxic response in coexposed zebrafish was also observed at the transcriptomic level. KEGG pathways analysis identified mitochondrial dysfunction in the intestine and metabolic disturbances in the liver. These results highlight the significance of mixture toxicity when studying the effects of NPs and associated chemicals like 6PPDq. | Combined Intestine | combined intestine 2 | strain:Wild type|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:laboratory|age:16 weeks|dev stage:adult|sex:male|tissue:intestine|biomaterial provider:not applicable|birth date:not applicable|birth location:not applicable|breeding history:not applicable|breeding method:not applicable|cell line:not applicable|cell subtype:not applicable|cell type:not applicable|collected by:Shubham Varshney|collection date:2023 06|culture collection:not applicable|death date:not applicable|disease:not applicable|disease stg:not applicable|genotype:not applicable|geo loc name:not applicable|growth protocol:not applicable|health state:not applicable|isolation source:not applicable|lat lon:not applicable|phenotype:not applicable|sample type:not applicable|specimen voucher:not applicable|store cond:not applicable|stud book number:not applicable|treatment:combined intestine replicate2|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | T8 2 | T8 2 | PCR enrichment of adaptor ligated DNA | RNA-Seq | TRANSCRIPTOMIC | PolyA | PAIRED | ILLUMINA | NextSeq 550 | SRP480720 | A43_1.fastq.gz A43_2.fastq.gz | fastq fastq | 7681997100.0 | 25606657.0 | A43 1.fastq.gz | 0:150 1:150 | A:2098281007;C:1758609887;G:1757658923;T:2067364339;N:82944 | 150 | 150 | 2098281007 | 1758609887 | 1757658923 | 2067364339 | 82944 | SRX23063705 | SRS20023727 | SRA1777576 | Nord University|Faculty of Biosciences and Aquaculture | Nord University | 2 | 0.92257 | 0.92131 | 0.07154 | 0.07125 | 0.74769 | 0.74712 | 0.52352 | 0.51843 | 150 | 150 | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | unknown | bulk | unknown | unknown | Norway | 2023-12-30 | Adult | Adult | Gut | Digestive System |