run_metadata: 33206

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
33206	SRR29848467	SRX25346224	SRS22013438	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.		pubmed:39742644		DMSO 120hpf eye replicate4	GSM8399276		source name:Dissected eye\|tissue:Dissected eye\|genotype:wildtype\|treatment:DMSO\|time:120hpf\|geo loc name:missing\|collection date:missing	DMSO 120hpf eye replicate4	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:DMSO\|time:120hpf	GSM8399276	GSM8399276: DMSO 120hpf eye replicate4; Danio rerio; RNA Seq	GSM8399276 r1	GSM8399276	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP520276			Ctrl_eye_4_1.fq.gz Ctrl_eye_4_2.fq.gz	fastq fastq	7198057200.0	23993524.0	GSM8399276 r1	0:150 1:150	A:1929066670;C:1680279530;G:1672121671;T:1910263876;N:6325453	150	150			1929066670	1680279530	1672121671	1910263876	6325453	SRX25346224	SRS22013438	SRA1925887	Dasgupta lab, Biological Sciences, Clemson University	Dasgupta lab, Biological Sciences, Clemson University	2	0.91947	0.90384	0.11309	0.11094	0.69576	0.69779	0.45803	0.45394	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		United States	2024-07-16	Multi-stage	Multi-stage	Eye	Sensory System