{"database": "metadata", "table": "run_metadata", "rows": [[33204, "SRR29848465", "SRX25346226", "SRS22013440", "SRP520276", "PRJNA1136505", "Assessing mechanisms driving phenol isopropylated phosphate IPP induced larval photomotor response deficits in zebrafish", "GSE272355", "Transcriptome Analysis", "Isopropylated phenyl phosphates IPP are an additive organophosphate flame retardant OPFR which has been extensively used in furniture  electronics  automobiles  plastics  and children's products to slow down the spread of fire. The processing and distribution of IPP  containing products have been prohibited but its continuous leaching from end use products has retained the concern of its toxicity. The present study was designed to evaluate IPP induced developmental toxicity using zebrafish embryos. We first performed  range finding experiments with embryonic zebrafish  exposed to 0   200 ?M IPP from 6 hpf to 120 hpf and found significant morphological impacts like pericardial edema  yolk sac edema and spinal curvature at higher concentrations. Following this  relying on secondary analyses of our whole embryo mRNA seq data  we quantified neurotransmitters and found significant increase in the levels of dopamine and its metabolite  3 methoxytyramine. We then conducted  in vitro retinoic acid receptor RAR signaling assay and noticed significant inhibition of RARa  but not RAR? and RAR?. For behavioral readouts  we performed larval photomotor response LPR assay at sublethal concentrations and observed hypoactive locomotory behavior in exposed larvae. Whole mount immunohistochemistry for 5 methylcytosine and global DNA methylation assay showed significant IPP induced hypermethylation in situ. Finally  based on whole embryo RNA seq data  we hypothesized that IPP affects the development of brain and eyes. Firstly  we performed global DNA methylation in brain and eyes  but did not find significant effects. Then  we conducted mRNA sequencing on dissected brains and eyes  and found 2 and 135 differentially expressed genes  respectively. Gene ontology revealed that IPP affect voltage gated ion channel activity  synaptic transmission and neurotransmitter signaling. Collectively  our data shows that IPP induces morphological abnormalities and disrupts larval photo motor response  potentially through RA inhibition and methylomic regulation. Finally  we observed that IPP affects gene expression within the developing eye  establishing synaptic transmission  vision and muscle contraction as a potential causative factor for LPR responses. Overall design: Zebrafish embryos were exposed to 0 or 0.2 uM IPP from 6 hpf to 120 hpf  eyes and brains were dissected out  RNA extraction and RNA sequencing using a Novogene Library preparation Pipeline and sequencing on an Novaseq 600 Illumina  San Diego  CA 2x150 bp  40m reads/sample.", null, "pubmed:39742644", null, "IPP 120hpf eye replicate2", "GSM8399278", null, "source name:Dissected eye|tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf|geo loc name:missing|collection date:missing", "IPP 120hpf eye replicate2", "Raw data raw reads in fastq format was firstly processed throughin house perl scripts. In this step  clean data clean reads was obtainedbyremoving reads containing adapter  reads containing ploy N and lowqualityreads from raw data. A Reference genome and gene model annotation files were downloadedfrom genome website directly. Index of the reference genome was built usingHisat2 v2.0.5 and paired end clean reads were aligned to the referencegenome using Hisat2 v2.0.5 FeatureCounts v1.5.0 p3 was used to count the reads numbers mappedto each gene. Then FPKM of each gene was calculated based on the lengthof the gene and reads count mapped to this gene. Differential expression analysisof two conditions/groups two biological replicates per condition was performed using the DESeq2R package 1.20.0. Assembly: GRZ11 Supplementary files format and content: Tab delimited txt file contains FPKM values for each sample", "Dissected eye", "Embryos were exposed to 0 or 0.2 uM IPP in 0.02% DMSO from 6 hpf to 120 hpf", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", "Embryos were spawned and maintained in system water", "tissue:Dissected eye|genotype:wildtype|treatment:IPP|time:120hpf", "GSM8399278", "GSM8399278: IPP 120hpf eye replicate2; Danio rerio; RNA Seq", "GSM8399278 r1", "GSM8399278", "1", "Eyes and brains were dissected from whole embryos  homogenized in  RNA zol  and RNA extraction was conducted using a Directzol RNA Miniprep Plus kit Zymo. RNA quality and quantity was validated using an Agilent Tapestation and Nanodrop. post fragmentation  the first strand cDNA was synthesized using random hexamer primers  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non directional library. For the non directional library  it was ready post end repair  A tailing  adapter ligation  size selection  amplification  and purification For the directional library  it was ready post end repair  A tailing  adapter ligation  size selection  USER enzyme digestion  amplification  and purification", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP520276", null, null, "IPP_eye_2_1.fq.gz IPP_eye_2_2.fq.gz", "fastq fastq", 7374435900.0, 24581453.0, "GSM8399278 r1", "0:150 1:150", "A:1986621253;C:1713862328;G:1699590477;T:1967874898;N:6486944", 150, 150, null, null, 1986621253, 1713862328, 1699590477, 1967874898, 6486944, "SRX25346226", "SRS22013440", "SRA1925887", "Dasgupta lab, Biological Sciences, Clemson University", "Dasgupta lab, Biological Sciences, Clemson University", 2, 0.9091, 0.90128, 0.11122, 0.1097, 0.70201, 0.70266, 0.44395, 0.4416, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-07-16", "Multi-stage", "Multi-stage", "Eye", "Sensory 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": ["33204"], "units": {}, "query_ms": 8.54308099951595}