run_metadata: 25835

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
25835	SRR25868751	SRX21590032	SRS18767603	SRP457982	PRJNA1011844	Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds	PRJNA1011844	Other	The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature bioaccumulation in organisms and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active in addition to the toxicity endpoints that best reflect chemical hazard. In this study zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control 1uM chlorpyrifos CAS 2921 88 2 positive control and eight concentrations 0 100 uM half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1 PFOA CAS 45285 51 6 and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf 6 hpf 48 hpf 24 hpf 48 hpf 6 hpf 120 hpf 24 hpf 120 hpf 48 hpf 120 hpf 96 hpf 120 hpf to assess how common experimental design variables e.g. different exposure durations exposure at different developmental stages affect point of departure estimates.					Pa9		strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56781\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep7\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa9 S254	Pa9 S254	At the end of each PFAS exposure period zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP457982			Pa9_S254_L003_R1_001.fastq.gz Pa9_S254_L003_R2_001.fastq.gz	fastq fastq	10318580700.0	34395269.0	Pa9 S254 L003 R1 001.fastq.gz	0:150 1:150	A:2688941742;C:2323349793;G:2732657504;T:2573540493;N:91168	150	150			2688941742	2323349793	2732657504	2573540493	91168	SRX21590032	SRS18767603	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58216	0.58922	0.07708	0.07964	0.72685	0.72541	0.47803	0.47944	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown		United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure