run_metadata: 35412
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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| 35412 | SRR32737856 | SRX28024075 | SRS24385628 | SRP570947 | PRJNA1237347 | Developmental opioid exposure results in lasting transcriptome alterations in zebrafish Danio rerio embryos | GSE292183 | Transcriptome Analysis | The opioid epidemic has introduced significant public health challenges with little knowledge regarding the consequences of opioid exposure during embryonic development. While neurobehavioral effects of developmental opioid exposure are well documented early effects of exposure remain largely unexplored. We investigated the effects of oxycodone and fentanyl exposure on gene expression in zebrafish Danio rerio embryos using whole embryo RNA sequencing. Embryos were exposed to environmentally relevant Oxycodone HCl 10.6pg/mL and Fentanyl Citrate 0.629pg/mL and therapeutically relevant Oxycodone HCl 35.14ng/mL and Fentanyl Citrate 3.14ng/mL from 2 hpf to 24 hpf followed by another 24hrs of opioid free development. RNA sequencing at 48hpf revealed dose and drug specific gene expression changes. Lower doses of oxycodone and fentanyl both induced more differentially expressed genes DEGs than higher doses potentially indicative of opioid receptor desensitization occurring at higher concentrations. In total 892 DEGs were identified across all conditions indicating continued differential gene expression well post cessation of opioid exposure. Gene ontology analysis revealed changes in gene expression relating to extracellular matrix ECM organization cell adhesion and visual and nervous system formation. Key pathways include axon guidance synapse formation and ECM biosynthesis/remodeling all of which have potential implications on neural connectivity and sensory development. These findings demonstrate that developmental exposure to opioids induced persistent transcriptomic changes which may have lasting implications for structural integrity and function in vertebrate nervous systems providing insights into the molecular mechanisms of opioid induced alterations during development. Overall design: Zebrafish embryos were exposed to one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL and oxycodone therapeutic OT; 35.14 ng/mL. Opioid exposure occurred from 0 hpf to 24 hpf in zebrafish embryos embryos were washed at 24hpf and allowed to develop in non opioid solution until 48 hpf. At 48hpf 50 embryos were sample were harvested for total RNA cDNA library prep and RNAseq. | pubmed:40429979 | replicate 6 control WT zebrafish 48hpf total RNA | GSM8851813 | source name:Total embryo 50 embryo homogenate|tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/22/2024|geo loc name:missing|collection date:missing | replicate 6 control WT zebrafish 48hpf total RNA | Sequenced by NovaGene via Novaseq X Plus Platform paired end reads Raw reads are available as the fq.gz files Trimmed via trimmomatic and ran through rCorrector then mapped to GRCz11 ensemble constructed reference library via Salmon. The aggregated count matrixes for each condition are availible as the txt files Assembly: These are raw reads from Novaseq X plus seqeuncing and count matrixes as txt files Supplementary files format and content: txt files of aggregated count matrixes see above Supplementary files format and content: the counts derived from Salmon | Total embryo 50 embryo homogenate | one of the following conditions: fentanyl effluent FE; 0.629 pg/mL fentanyl therapeutic FT; 3.14 ng/mL oxycodone effluent OE; 10.6 pg/mL oxycodone therapeutic OT; 35.14 ng/mL Control. Opioid exposed embryos were exposed from xxx ttwo xxx hpf. At 24 hpf embryos were washed to remove opioids and allowed to develop normally until 48 hpf. | Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003 | zebrafish embryos were maintained in 0.3x Danieau solution at 28.5C | tissue:Total embryo 50 embryo homogenate|genotype:WT|treatment:N1|batch:8/22/2024 | GSM8851813 | GSM8851813: replicate 6 control WT zebrafish 48hpf total RNA; Danio rerio; RNA Seq | GSM8851813 r1 | GSM8851813 | 1 | Trizol Chloroform extraction of total RNA followed by Dnase I treatment and Monarch RNA cleanup kit T2030L. All samples were confirmed to have A260/A280 ratios between 1.8 and 2.0 on Nanodrop spectrophotometer. All samples were confirmed to have RNA integrity numbers of above 7 via Agilent Bioanalyzer 2100 Zymo Seq RiboFree Total RNA library Kit R30003 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq X Plus | SRP570947 | R2Control_CKDL240028231-1A_22NFN3LT3_L7_1.fq.gz R2Control_CKDL240028231-1A_22NFN3LT3_L7_2.fq.gz | fastq fastq | 14617714200.0 | 48725714.0 | GSM8851813 r1 | 0:150 1:150 | A:3998241249;C:3282188059;G:3287516949;T:4049030965;N:736978 | 150 | 150 | 3998241249 | 3282188059 | 3287516949 | 4049030965 | 736978 | SRX28024075 | SRS24385628 | SRA2094947 | Merzdorf, MCB, Montana State University | Merzdorf, MCB, Montana State University | B | B | biological fallback assumption | illumina | novaseq_era | unknown | random_priming | unknown | bulk | bulk | bulk | United States | 2025-03-17 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures |