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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
24645 SRR25475241 SRX21207438 SRS18464907 SRP452529 PRJNA1000943 Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl ethyl and propyl parabens in zebrafish embryos GSE239773 Transcriptome Analysis Limited studies on comparison of developmental neurotoxicity of parabens have been conducted and unharmonized concentrations between phenotypic observations and transcriptomic analysis hamper understanding of their differential molecular mechanism. Developmental toxicity testing was conducted with commonly used methyl MtP ethyl EtP and propyl paraben PrP in zebrafish embryos. Based on benchmark dose 5% BMD5 embryonic mortality based point of departure M PoD values of three parabens were determined and changes in locomotor behavior were evaluated at concentrations of 0 M PoD/50 M PoD/10 and M PoD in which transcriptomic analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long chained parabens were more toxic than short chained parabens as determined by M PoD values of 154.1 72.6 and 24.2 µM for MtP EtP and PrP respectively. While exposure to EtP resulted in hyperactivity no behavior effect was observed by MtP and PrP. Transcriptomics analysis revealed that abnormal behaviors in EtP exposed group are associated with the distinctly enriched pathways in signal transport calcium ion binding and metal binding. In contrast exposure to MtP and PrP mainly disrupted the membrane and transmembrane which are closely linked to abnormal embryonic development rather than neurobehavior changes. According to the changes in expression of signature mRNAs tentative transcriptomic based PoD T PoD values for each paraben were determined as MtP 2.68 µM EtP 3.85 µM and PrP 1.4 µM. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish Danio rerio. This study was supported by Korea Environment Industry & Technology Institute KEITI through "the Technology Development Project for Safety Management of Household Chemical Products" funded by Korea Ministry of Environment MOE grant number 2020002960006.       Zebrafish MtP BMD5 [MtP BMD5 1] GSM7671209   source name:Whole body|strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5|geo loc name:missing|collection date:missing Zebrafish MtP BMD5 [MtP BMD5 1] Filtered reads quality >20 and length >50 were aligned to the Ensembl reference genome on Danio rerio GCA 000002035.4. Assembly: GCA 000002035.4 Supplementary files format and content: RPKM TPM values Whole body   The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library   strain:AB wild type|tissue:Whole body|developmental stage:120 hpf|treatment:MtP BMD5 GSM7671209 GSM7671209: Zebrafish MtP BMD5 [MtP BMD5 1]; Danio rerio; RNA Seq GSM7671209 r1 GSM7671209 1 The RNA extraction was conducted with RNAzol® reagent Molecular Research Center Inc. Cincinnati OH USA and appropriate amounts >200 ng of RNA were obtained. A KAPA Library Quantification Kit was used to quantify the sequencing library   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP452529   loader:fastq load.py MtP_BMD5_1_1.fq.gz MtP_BMD5_1_4.fq.gz fastq fastq 4052874428.0 13420114.0 GSM7671209 r1 0:151 1:151 A:1131227099;C:867529007;G:1014888508;T:1039101737;N:128077 151 151     1131227099 867529007 1014888508 1039101737 128077 SRX21207438 SRS18464907 SRA1684601 Seoul National University of Science and Technology Seoul National University of Science and Technology 2 0.94427 0.94289 0.11676 0.11646 0.71587 0.72013 0.4544 0.45822 151 151 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified unknown bulk unknown unknown   South Korea 2023-08-01 Larval Larval Trunk Surface Structure