metadata: run_metadata: 1,771 rows where devstage_curation_coarse = "Embryo" and tissue

1,771 rows where devstage_curation_coarse = "Embryo" and tissue_curation = "Trunk"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
25376	25376	SRR25868914	SRX21590491	SRS18768063	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.	T1Ad1	strain:AB wild type\|age:6 24hpf\|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 56229\|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:1\|dose:1687.3254831396318\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad1 S259	T1Ad1 S259	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	T1Ad1_S259_L003_R1_001.fastq.gz T1Ad1_S259_L003_R2_001.fastq.gz	fastq fastq	7819723500.0	26065745.0	T1Ad1 S259 L003 R1 001.fastq.gz	0:150 1:150	A:2031599001;C:1759639807;G:2105335746;T:1923080206;N:68740	150	150	2031599001	1759639807	2105335746	1923080206	68740	SRX21590491	SRS18768063	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59547	0.59971	0.05855	0.05976	0.74332	0.74477	0.48103	0.48162	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25377	25377	SRR25868915	SRX21590490	SRS18768064	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.	T1Ac5	strain:AB wild type\|age:6 24hpf\|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 56228\|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:1\|dose:6461.39165470093\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ac5 S5	T1Ac5 S5	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	T1Ac5_S5_L001_R1_001.fastq.gz T1Ac5_S5_L001_R2_001.fastq.gz	fastq fastq	7625048100.0	25416827.0	T1Ac5 S5 L001 R1 001.fastq.gz	0:150 1:150	A:1966966252;C:1726081062;G:2022524018;T:1909426914;N:49854	150	150	1966966252	1726081062	2022524018	1909426914	49854	SRX21590490	SRS18768064	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59676	0.60268	0.06216	0.0642	0.74174	0.74113	0.47678	0.47717	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25378	25378	SRR25868916	SRX21590489	SRS18768062	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.	T1Ac4	strain:AB wild type\|age:6 24hpf\|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 56227\|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:1\|dose:6461.39165470093\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ac4 S383	T1Ac4 S383	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	T1Ac4_S383_L004_R1_001.fastq.gz T1Ac4_S383_L004_R2_001.fastq.gz	fastq fastq	6653231400.0	22177438.0	T1Ac4 S383 L004 R1 001.fastq.gz	0:150 1:150	A:1736107768;C:1497492478;G:1749793425;T:1669780748;N:56981	150	150	1736107768	1497492478	1749793425	1669780748	56981	SRX21590489	SRS18768062	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6438	0.64822	0.06467	0.06566	0.73742	0.73807	0.47559	0.47987	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25379	25379	SRR25868917	SRX21590488	SRS18768061	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.	T1Ac3	strain:AB wild type\|age:6 24hpf\|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 56226\|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:1\|dose:6461.39165470093\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ac3 S132	T1Ac3 S132	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	T1Ac3_S132_L002_R1_001.fastq.gz T1Ac3_S132_L002_R2_001.fastq.gz	fastq fastq	4826356500.0	16087855.0	T1Ac3 S132 L002 R1 001.fastq.gz	0:150 1:150	A:1255196359;C:1087160424;G:1291949396;T:1192013773;N:36548	150	150	1255196359	1087160424	1291949396	1192013773	36548	SRX21590488	SRS18768061	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63006	0.63488	0.06653	0.06719	0.74235	0.74207	0.47463	0.47853	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25380	25380	SRR25868918	SRX21590487	SRS18768060	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.	T1Ac2	strain:AB wild type\|age:6 24hpf\|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 56225\|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:1\|dose:6461.39165470093\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ac2 S4	T1Ac2 S4	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	T1Ac2_S4_L001_R1_001.fastq.gz T1Ac2_S4_L001_R2_001.fastq.gz	fastq fastq	5236125600.0	17453752.0	T1Ac2 S4 L001 R1 001.fastq.gz	0:150 1:150	A:1364663796;C:1155880460;G:1404167486;T:1311305290;N:108568	150	150	1364663796	1155880460	1404167486	1311305290	108568	SRX21590487	SRS18768060	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57127	0.5764	0.05133	0.05264	0.74815	0.74789	0.46551	0.46517	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25381	25381	SRR25868919	SRX21590486	SRS18768057	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.	T1Ac1	strain:AB wild type\|age:6 24hpf\|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 56224\|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:1\|dose:6461.39165470093\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ac1 S258	T1Ac1 S258	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	T1Ac1_S258_L003_R1_001.fastq.gz T1Ac1_S258_L003_R2_001.fastq.gz	fastq fastq	5556495600.0	18521652.0	T1Ac1 S258 L003 R1 001.fastq.gz	0:150 1:150	A:1456422234;C:1242170020;G:1458160272;T:1399693066;N:50008	150	150	1456422234	1242170020	1458160272	1399693066	50008	SRX21590486	SRS18768057	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60445	0.61015	0.06801	0.06934	0.74363	0.74318	0.46687	0.46545	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25382	25382	SRR25868920	SRX21590485	SRS18768059	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.	T3VAd4	strain:AB wild type\|age:24 48hpf\|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 55846\|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:3\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T3VAd4 S54	T3VAd4 S54	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	T3VAd4_S54_L001_R1_001.fastq.gz T3VAd4_S54_L001_R2_001.fastq.gz	fastq fastq	7031356200.0	23437854.0	T3VAd4 S54 L001 R1 001.fastq.gz	0:150 1:150	A:1829545875;C:1587218347;G:1846841433;T:1767607602;N:142943	150	150	1829545875	1587218347	1846841433	1767607602	142943	SRX21590485	SRS18768059	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63681	0.63976	0.0648	0.06627	0.73726	0.73797	0.458	0.44913	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25383	25383	SRR25868921	SRX21590484	SRS18768056	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.	T1Ab5 rep	strain:AB wild type\|age:6 24hpf\|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 56223\|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:1\|dose:15875\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep7\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab5 rep S12	T1Ab5 rep S12	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	T1Ab5_rep_S12_L003_R1_001.fastq.gz T1Ab5_rep_S12_L003_R2_001.fastq.gz	fastq fastq	4397784600.0	14659282.0	T1Ab5 rep S12 L003 R1 001.fastq.gz	0:150 1:150	A:1153896712;C:974272119;G:1161879342;T:1107669639;N:66788	150	150	1153896712	974272119	1161879342	1107669639	66788	SRX21590484	SRS18768056	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59862	0.60718	0.05947	0.06101	0.74375	0.74162	0.47548	0.47307	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25384	25384	SRR25868922	SRX21590483	SRS18768058	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.	T1Ab5	strain:AB wild type\|age:6 24hpf\|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 56222\|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:1\|dose:15874.98692280121\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep6\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab5 S382	T1Ab5 S382	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	T1Ab5_S382_L004_R1_001.fastq.gz T1Ab5_S382_L004_R2_001.fastq.gz	fastq fastq	6666980400.0	22223268.0	T1Ab5 S382 L004 R1 001.fastq.gz	0:150 1:150	A:1737129131;C:1487358347;G:1760951097;T:1681485762;N:56063	150	150	1737129131	1487358347	1760951097	1681485762	56063	SRX21590483	SRS18768058	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62494	0.63201	0.06044	0.06182	0.74014	0.73947	0.47277	0.47697	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25385	25385	SRR25868923	SRX21590482	SRS18768055	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.	T1Ab4 rep	strain:AB wild type\|age:6 24hpf\|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 56221\|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:1\|dose:15874.98692280121\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep5\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab4 rep S158	T1Ab4 rep S158	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	T1Ab4_rep_S158_L002_R1_001.fastq.gz T1Ab4_rep_S158_L002_R2_001.fastq.gz	fastq fastq	5522588700.0	18408629.0	T1Ab4 rep S158 L002 R1 001.fastq.gz	0:150 1:150	A:1424629799;C:1243915555;G:1480819588;T:1373109378;N:114380	150	150	1424629799	1243915555	1480819588	1373109378	114380	SRX21590482	SRS18768055	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.5782	0.58536	0.05154	0.05276	0.7474	0.74631	0.46697	0.47676	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25386	25386	SRR25868924	SRX21590481	SRS18768053	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.	T2VBe5	strain:AB wild type\|age:6 48hpf\|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 55837\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep18\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VBe5 S290	T2VBe5 S290	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	T2VBe5_S290_L003_R1_001.fastq.gz T2VBe5_S290_L003_R2_001.fastq.gz	fastq fastq	9043268100.0	30144227.0	T2VBe5 S290 L003 R1 001.fastq.gz	0:150 1:150	A:2380557635;C:2035880450;G:2333617678;T:2293130816;N:81521	150	150	2380557635	2035880450	2333617678	2293130816	81521	SRX21590481	SRS18768053	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62739	0.63483	0.06826	0.0704	0.73158	0.73077	0.45973	0.46278	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25397	25397	SRR25868935	SRX21590470	SRS18768043	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.	T2VBd4	strain:AB wild type\|age:6 48hpf\|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 55836\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep17\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VBd4 S37	T2VBd4 S37	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	T2VBd4_S37_L001_R1_001.fastq.gz T2VBd4_S37_L001_R2_001.fastq.gz	fastq fastq	7009117200.0	23363724.0	T2VBd4 S37 L001 R1 001.fastq.gz	0:150 1:150	A:1823367857;C:1614584828;G:1813830528;T:1757193239;N:140748	150	150	1823367857	1614584828	1813830528	1757193239	140748	SRX21590470	SRS18768043	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.68764	0.69107	0.06752	0.06853	0.72841	0.72918	0.4631	0.46148	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25405	25405	SRR25868943	SRX21590462	SRS18768035	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.	T3Hh5	strain:AB wild type\|age:24 48hpf\|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 56044\|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:3\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hh5 S53	T3Hh5 S53	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	T3Hh5_S53_L001_R1_001.fastq.gz T3Hh5_S53_L001_R2_001.fastq.gz	fastq fastq	8606654100.0	28688847.0	T3Hh5 S53 L001 R1 001.fastq.gz	0:150 1:150	A:2247227470;C:1972559832;G:2196464086;T:2190223477;N:179235	150	150	2247227470	1972559832	2196464086	2190223477	179235	SRX21590462	SRS18768035	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.73217	0.74291	0.10019	0.10397	0.72523	0.7248	0.47319	0.48192	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25406	25406	SRR25868944	SRX21590461	SRS18768034	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.	T2VAg7	strain:AB wild type\|age:6 48hpf\|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 55828\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep9\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VAg7 S55	T2VAg7 S55	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	T2VAg7_S55_L001_R1_001.fastq.gz T2VAg7_S55_L001_R2_001.fastq.gz	fastq fastq	4361456100.0	14538187.0	T2VAg7 S55 L001 R1 001.fastq.gz	0:150 1:150	A:1123667735;C:997475580;G:1166529499;T:1073687884;N:95402	150	150	1123667735	997475580	1166529499	1073687884	95402	SRX21590461	SRS18768034	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62528	0.63278	0.07333	0.07481	0.7419	0.74002	0.47098	0.48068	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25407	25407	SRR25868945	SRX21590460	SRS18768033	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.	T3Hh4	strain:AB wild type\|age:24 48hpf\|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 56043\|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:3\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hh4 S432	T3Hh4 S432	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	T3Hh4_S432_L004_R1_001.fastq.gz T3Hh4_S432_L004_R2_001.fastq.gz	fastq fastq	5996049000.0	19986830.0	T3Hh4 S432 L004 R1 001.fastq.gz	0:150 1:150	A:1594748177;C:1334406026;G:1516531755;T:1550309432;N:53610	150	150	1594748177	1334406026	1516531755	1550309432	53610	SRX21590460	SRS18768033	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6314	0.63991	0.08444	0.08723	0.7359	0.7359	0.47103	0.46802	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25408	25408	SRR25868946	SRX21590459	SRS18768032	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.	T3Hh3	strain:AB wild type\|age:24 48hpf\|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 56042\|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:3\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hh3 S213	T3Hh3 S213	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	T3Hh3_S213_L002_R1_001.fastq.gz T3Hh3_S213_L002_R2_001.fastq.gz	fastq fastq	4935489600.0	16451632.0	T3Hh3 S213 L002 R1 001.fastq.gz	0:150 1:150	A:1293150279;C:1118734612;G:1253582650;T:1269917881;N:104178	150	150	1293150279	1118734612	1253582650	1269917881	104178	SRX21590459	SRS18768032	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66755	0.67797	0.09506	0.09706	0.73568	0.73442	0.48682	0.48525	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25409	25409	SRR25868947	SRX21590458	SRS18768026	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.	T3Hh2	strain:AB wild type\|age:24 48hpf\|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 56041\|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:3\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hh2 S181	T3Hh2 S181	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	T3Hh2_S181_L002_R1_001.fastq.gz T3Hh2_S181_L002_R2_001.fastq.gz	fastq fastq	6136300500.0	20454335.0	T3Hh2 S181 L002 R1 001.fastq.gz	0:150 1:150	A:1573808613;C:1410149163;G:1628578278;T:1523720287;N:44159	150	150	1573808613	1410149163	1628578278	1523720287	44159	SRX21590458	SRS18768026	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64849	0.65461	0.10125	0.10345	0.7418	0.74172	0.48625	0.48551	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25410	25410	SRR25868948	SRX21590457	SRS18768031	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.	T3Hh1	strain:AB wild type\|age:24 48hpf\|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 56040\|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:3\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hh1 S85	T3Hh1 S85	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	T3Hh1_S85_L001_R1_001.fastq.gz T3Hh1_S85_L001_R2_001.fastq.gz	fastq fastq	5334105300.0	17780351.0	T3Hh1 S85 L001 R1 001.fastq.gz	0:150 1:150	A:1392076110;C:1201900262;G:1387222272;T:1352791891;N:114765	150	150	1392076110	1201900262	1387222272	1352791891	114765	SRX21590457	SRS18768031	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6323	0.64164	0.07669	0.0783	0.73783	0.73594	0.46426	0.46817	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25411	25411	SRR25868949	SRX21590456	SRS18768030	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.	T3Hg5	strain:AB wild type\|age:24 48hpf\|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 56039\|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:3\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hg5 S52	T3Hg5 S52	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	T3Hg5_S52_L001_R1_001.fastq.gz T3Hg5_S52_L001_R2_001.fastq.gz	fastq fastq	9438714000.0	31462380.0	T3Hg5 S52 L001 R1 001.fastq.gz	0:150 1:150	A:2474985851;C:2154357872;G:2391311229;T:2417865761;N:193287	150	150	2474985851	2154357872	2391311229	2417865761	193287	SRX21590456	SRS18768030	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.54287	0.72194	0.06976	0.09635	0.7503	0.72839	0.47769	0.48654	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25412	25412	SRR25868950	SRX21590455	SRS18768028	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.	T3Hg4	strain:AB wild type\|age:24 48hpf\|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 56038\|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:3\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hg4 S212	T3Hg4 S212	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	T3Hg4_S212_L002_R1_001.fastq.gz T3Hg4_S212_L002_R2_001.fastq.gz	fastq fastq	6358528500.0	21195095.0	T3Hg4 S212 L002 R1 001.fastq.gz	0:150 1:150	A:1650846535;C:1450024091;G:1666736610;T:1590789977;N:131287	150	150	1650846535	1450024091	1666736610	1590789977	131287	SRX21590455	SRS18768028	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6529	0.66224	0.06898	0.07053	0.73561	0.73499	0.46115	0.46487	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25413	25413	SRR25868951	SRX21590454	SRS18768027	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.	T3Hg3	strain:AB wild type\|age:24 48hpf\|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 56037\|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:3\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hg3 S431	T3Hg3 S431	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	T3Hg3_S431_L004_R1_001.fastq.gz T3Hg3_S431_L004_R2_001.fastq.gz	fastq fastq	7007539500.0	23358465.0	T3Hg3 S431 L004 R1 001.fastq.gz	0:150 1:150	A:1840370367;C:1592634131;G:1771518491;T:1802960225;N:56286	150	150	1840370367	1592634131	1771518491	1802960225	56286	SRX21590454	SRS18768027	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6848	0.69485	0.08494	0.08786	0.73016	0.73095	0.47207	0.47738	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25414	25414	SRR25868952	SRX21590453	SRS18768029	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.	T3Hg2	strain:AB wild type\|age:24 48hpf\|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 56036\|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:3\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hg2 S84	T3Hg2 S84	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	T3Hg2_S84_L001_R1_001.fastq.gz T3Hg2_S84_L001_R2_001.fastq.gz	fastq fastq	5953142100.0	19843807.0	T3Hg2 S84 L001 R1 001.fastq.gz	0:150 1:150	A:1547844763;C:1353300917;G:1546150907;T:1505715498;N:130015	150	150	1547844763	1353300917	1546150907	1505715498	130015	SRX21590453	SRS18768029	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63035	0.64008	0.07369	0.07592	0.73438	0.73413	0.45946	0.46548	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25415	25415	SRR25868953	SRX21590452	SRS18768025	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.	T3Hg1	strain:AB wild type\|age:24 48hpf\|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 56035\|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:3\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hg1 S180	T3Hg1 S180	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	T3Hg1_S180_L002_R1_001.fastq.gz T3Hg1_S180_L002_R2_001.fastq.gz	fastq fastq	7007395800.0	23357986.0	T3Hg1 S180 L002 R1 001.fastq.gz	0:150 1:150	A:1797987026;C:1593832268;G:1917307854;T:1698216898;N:51754	150	150	1797987026	1593832268	1917307854	1698216898	51754	SRX21590452	SRS18768025	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59524	0.59679	0.06376	0.06447	0.74726	0.74817	0.45641	0.45744	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25416	25416	SRR25868954	SRX21590451	SRS18768024	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.	T3Hf5	strain:AB wild type\|age:24 48hpf\|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 56034\|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:3\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T3Hf5 S51	T3Hf5 S51	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	T3Hf5_S51_L001_R1_001.fastq.gz T3Hf5_S51_L001_R2_001.fastq.gz	fastq fastq	8594460300.0	28648201.0	T3Hf5 S51 L001 R1 001.fastq.gz	0:150 1:150	A:2246923557;C:1934746915;G:2236327639;T:2176290460;N:171729	150	150	2246923557	1934746915	2236327639	2176290460	171729	SRX21590451	SRS18768024	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63438	0.64238	0.07368	0.07626	0.7374	0.73588	0.46742	0.471	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25417	25417	SRR25868955	SRX21590450	SRS18768023	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.	T2VAf6 rep	strain:AB wild type\|age:6 48hpf\|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 55827\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep8\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VAf6 rep S103	T2VAf6 rep S103	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	T2VAf6_rep_S103_L003_R1_001.fastq.gz T2VAf6_rep_S103_L003_R2_001.fastq.gz	fastq fastq	5532020400.0	18440068.0	T2VAf6 rep S103 L003 R1 001.fastq.gz	0:150 1:150	A:1438950484;C:1236393571;G:1459451658;T:1397138116;N:86571	150	150	1438950484	1236393571	1459451658	1397138116	86571	SRX21590450	SRS18768023	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58367	0.5922	0.06559	0.06776	0.73758	0.73683	0.47136	0.47059	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25418	25418	SRR25868956	SRX21590449	SRS18768021	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.	T2VAd4	strain:AB wild type\|age:6 48hpf\|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 55824\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VAd4 S90	T2VAd4 S90	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	T2VAd4_S90_L003_R1_001.fastq.gz T2VAd4_S90_L003_R2_001.fastq.gz	fastq fastq	4543459800.0	15144866.0	T2VAd4 S90 L003 R1 001.fastq.gz	0:150 1:150	A:1168350671;C:1024750476;G:1221048681;T:1129241549;N:68423	150	150	1168350671	1024750476	1221048681	1129241549	68423	SRX21590449	SRS18768021	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59826	0.60379	0.05883	0.06027	0.73732	0.73693	0.46171	0.45841	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25419	25419	SRR25868957	SRX21590448	SRS18768019	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.	T1VAc3	strain:AB wild type\|age:6 24hpf\|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 55806\|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:1\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VAc3 S118	T1VAc3 S118	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	T1VAc3_S118_L001_R1_001.fastq.gz T1VAc3_S118_L001_R2_001.fastq.gz	fastq fastq	6238113900.0	20793713.0	T1VAc3 S118 L001 R1 001.fastq.gz	0:150 1:150	A:1644198157;C:1386918863;G:1644152299;T:1562708182;N:136399	150	150	1644198157	1386918863	1644152299	1562708182	136399	SRX21590448	SRS18768019	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59634	0.60501	0.04872	0.05012	0.73998	0.73977	0.46562	0.46987	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25420	25420	SRR25868958	SRX21590447	SRS18768022	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.	T2Hh5	strain:AB wild type\|age:6 48hpf\|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 56003\|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:2\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hh5 S414	T2Hh5 S414	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	T2Hh5_S414_L004_R1_001.fastq.gz T2Hh5_S414_L004_R2_001.fastq.gz	fastq fastq	6363501300.0	21211671.0	T2Hh5 S414 L004 R1 001.fastq.gz	0:150 1:150	A:1633200988;C:1463291115;G:1668328317;T:1598626113;N:54767	150	150	1633200988	1463291115	1668328317	1598626113	54767	SRX21590447	SRS18768022	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6552	0.66277	0.08313	0.08511	0.73914	0.73878	0.48449	0.48569	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25421	25421	SRR25868959	SRX21590446	SRS18768020	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.	T2Hh3	strain:AB wild type\|age:6 48hpf\|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 56002\|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:2\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hh3 S205	T2Hh3 S205	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	T2Hh3_S205_L002_R1_001.fastq.gz T2Hh3_S205_L002_R2_001.fastq.gz	fastq fastq	5153181000.0	17177270.0	T2Hh3 S205 L002 R1 001.fastq.gz	0:150 1:150	A:1311909387;C:1193666264;G:1363654325;T:1283845021;N:106003	150	150	1311909387	1193666264	1363654325	1283845021	106003	SRX21590446	SRS18768020	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57789	0.58519	0.06221	0.06327	0.75069	0.74937	0.47035	0.46267	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25422	25422	SRR25868960	SRX21590445	SRS18768017	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.	T2Hh2	strain:AB wild type\|age:6 48hpf\|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 56001\|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:2\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hh2 S35	T2Hh2 S35	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	T2Hh2_S35_L001_R1_001.fastq.gz T2Hh2_S35_L001_R2_001.fastq.gz	fastq fastq	5343946500.0	17813155.0	T2Hh2 S35 L001 R1 001.fastq.gz	0:150 1:150	A:1376925806;C:1221257574;G:1409631094;T:1336024569;N:107457	150	150	1376925806	1221257574	1409631094	1336024569	107457	SRX21590445	SRS18768017	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64532	0.65232	0.0756	0.07835	0.73578	0.73604	0.4724	0.47406	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25423	25423	SRR25868961	SRX21590444	SRS18768018	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.	T2Hh1	strain:AB wild type\|age:6 48hpf\|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 56000\|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:2\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hh1 S163	T2Hh1 S163	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	T2Hh1_S163_L002_R1_001.fastq.gz T2Hh1_S163_L002_R2_001.fastq.gz	fastq fastq	6496199700.0	21653999.0	T2Hh1 S163 L002 R1 001.fastq.gz	0:150 1:150	A:1654255900;C:1491651654;G:1768642591;T:1581603217;N:46338	150	150	1654255900	1491651654	1768642591	1581603217	46338	SRX21590444	SRS18768018	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62024	0.62515	0.07791	0.07921	0.74854	0.74961	0.47833	0.4787	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25424	25424	SRR25868962	SRX21590443	SRS18768016	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.	T2Hg5	strain:AB wild type\|age:6 48hpf\|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 55999\|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:2\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hg5 S204	T2Hg5 S204	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	T2Hg5_S204_L002_R1_001.fastq.gz T2Hg5_S204_L002_R2_001.fastq.gz	fastq fastq	5012672100.0	16708907.0	T2Hg5 S204 L002 R1 001.fastq.gz	0:150 1:150	A:1311418541;C:1115411873;G:1326005358;T:1259732874;N:103454	150	150	1311418541	1115411873	1326005358	1259732874	103454	SRX21590443	SRS18768016	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61803	0.62477	0.07393	0.07563	0.74109	0.74142	0.46231	0.46386	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25425	25425	SRR25868963	SRX21590442	SRS18768015	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.	T2Hg4	strain:AB wild type\|age:6 48hpf\|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 55998\|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:2\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hg4 S76	T2Hg4 S76	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	T2Hg4_S76_L001_R1_001.fastq.gz T2Hg4_S76_L001_R2_001.fastq.gz	fastq fastq	5694816900.0	18982723.0	T2Hg4 S76 L001 R1 001.fastq.gz	0:150 1:150	A:1472278778;C:1298911619;G:1476566935;T:1446934449;N:125119	150	150	1472278778	1298911619	1476566935	1446934449	125119	SRX21590442	SRS18768015	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63996	0.65047	0.08134	0.08323	0.73736	0.73612	0.48563	0.48096	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25426	25426	SRR25868964	SRX21590441	SRS18768014	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.	T2Hg3	strain:AB wild type\|age:6 48hpf\|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 55997\|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:2\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hg3 S413	T2Hg3 S413	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	T2Hg3_S413_L004_R1_001.fastq.gz T2Hg3_S413_L004_R2_001.fastq.gz	fastq fastq	7675664400.0	25585548.0	T2Hg3 S413 L004 R1 001.fastq.gz	0:150 1:150	A:1960732294;C:1759892833;G:2021602153;T:1933370959;N:66161	150	150	1960732294	1759892833	2021602153	1933370959	66161	SRX21590441	SRS18768014	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64576	0.65335	0.07734	0.07935	0.73902	0.73858	0.47501	0.47742	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25427	25427	SRR25868965	SRX21590440	SRS18768010	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.	T2Hg2	strain:AB wild type\|age:6 48hpf\|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 55996\|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:2\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hg2 S34	T2Hg2 S34	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	T2Hg2_S34_L001_R1_001.fastq.gz T2Hg2_S34_L001_R2_001.fastq.gz	fastq fastq	7311786300.0	24372621.0	T2Hg2 S34 L001 R1 001.fastq.gz	0:150 1:150	A:1822000110;C:1662047492;G:2040172567;T:1787419473;N:146658	150	150	1822000110	1662047492	2040172567	1787419473	146658	SRX21590440	SRS18768010	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63219	0.63502	0.06283	0.06435	0.73783	0.73754	0.45634	0.45703	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25428	25428	SRR25868966	SRX21590439	SRS18768012	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.	T2Hg1	strain:AB wild type\|age:6 48hpf\|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 55995\|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:2\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hg1 S162	T2Hg1 S162	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	T2Hg1_S162_L002_R1_001.fastq.gz T2Hg1_S162_L002_R2_001.fastq.gz	fastq fastq	4917164100.0	16390547.0	T2Hg1 S162 L002 R1 001.fastq.gz	0:150 1:150	A:1267540801;C:1148223297;G:1274723166;T:1226642409;N:34427	150	150	1267540801	1148223297	1274723166	1226642409	34427	SRX21590439	SRS18768012	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.73385	0.73825	0.08809	0.09002	0.73797	0.73789	0.45386	0.46206	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25429	25429	SRR25868967	SRX21590438	SRS18768008	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.	T2Hf5	strain:AB wild type\|age:6 48hpf\|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 55994\|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:2\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hf5 S75	T2Hf5 S75	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	T2Hf5_S75_L001_R1_001.fastq.gz T2Hf5_S75_L001_R2_001.fastq.gz	fastq fastq	5409247800.0	18030826.0	T2Hf5 S75 L001 R1 001.fastq.gz	0:150 1:150	A:1424189636;C:1215228317;G:1390359173;T:1379353846;N:116828	150	150	1424189636	1215228317	1390359173	1379353846	116828	SRX21590438	SRS18768008	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65634	0.66603	0.07004	0.07227	0.73474	0.73405	0.44749	0.4504	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25430	25430	SRR25868968	SRX21590437	SRS18768013	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.	T2VAc3	strain:AB wild type\|age:6 48hpf\|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 55823\|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:2\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T2VAc3 S415	T2VAc3 S415	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	T2VAc3_S415_L004_R1_001.fastq.gz T2VAc3_S415_L004_R2_001.fastq.gz	fastq fastq	7527453000.0	25091510.0	T2VAc3 S415 L004 R1 001.fastq.gz	0:150 1:150	A:1979535018;C:1682398865;G:1905921289;T:1959534715;N:63113	150	150	1979535018	1682398865	1905921289	1959534715	63113	SRX21590437	SRS18768013	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.69358	0.70306	0.08181	0.08557	0.72165	0.72149	0.46112	0.46042	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25431	25431	SRR25868969	SRX21590436	SRS18768011	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.	T2Hf4	strain:AB wild type\|age:6 48hpf\|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 55993\|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:2\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hf4 S203	T2Hf4 S203	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	T2Hf4_S203_L002_R1_001.fastq.gz T2Hf4_S203_L002_R2_001.fastq.gz	fastq fastq	4545658500.0	15152195.0	T2Hf4 S203 L002 R1 001.fastq.gz	0:150 1:150	A:1216340474;C:997497986;G:1183202312;T:1148520160;N:97568	150	150	1216340474	997497986	1183202312	1148520160	97568	SRX21590436	SRS18768011	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61974	0.62795	0.07493	0.07716	0.73641	0.73588	0.4715	0.47178	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25432	25432	SRR25868970	SRX21590435	SRS18768009	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.	T2Hf3	strain:AB wild type\|age:6 48hpf\|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 55992\|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:2\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hf3 S412	T2Hf3 S412	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	T2Hf3_S412_L004_R1_001.fastq.gz T2Hf3_S412_L004_R2_001.fastq.gz	fastq fastq	8138978700.0	27129929.0	T2Hf3 S412 L004 R1 001.fastq.gz	0:150 1:150	A:2123779813;C:1838531052;G:2114568794;T:2062028054;N:70987	150	150	2123779813	1838531052	2114568794	2062028054	70987	SRX21590435	SRS18768009	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6665	0.67651	0.08104	0.083	0.73229	0.7304	0.4665	0.47002	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25433	25433	SRR25868971	SRX21590434	SRS18768007	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.	T2Hf2	strain:AB wild type\|age:6 48hpf\|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 55991\|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:2\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T2Hf2 S33	T2Hf2 S33	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	T2Hf2_S33_L001_R1_001.fastq.gz T2Hf2_S33_L001_R2_001.fastq.gz	fastq fastq	5747110800.0	19157036.0	T2Hf2 S33 L001 R1 001.fastq.gz	0:150 1:150	A:1498440942;C:1293347475;G:1516806631;T:1438395933;N:119819	150	150	1498440942	1293347475	1516806631	1438395933	119819	SRX21590434	SRS18768007	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67541	0.67945	0.07229	0.07367	0.73261	0.73365	0.47036	0.47568	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25434	25434	SRR25868972	SRX21590433	SRS18768006	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.	T1Hh3	strain:AB wild type\|age:6 24hpf\|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 55961\|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:1\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hh3 S396	T1Hh3 S396	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	T1Hh3_S396_L004_R1_001.fastq.gz T1Hh3_S396_L004_R2_001.fastq.gz	fastq fastq	6527251500.0	21757505.0	T1Hh3 S396 L004 R1 001.fastq.gz	0:150 1:150	A:1683618490;C:1484446987;G:1740844350;T:1618285311;N:56362	150	150	1683618490	1484446987	1740844350	1618285311	56362	SRX21590433	SRS18768006	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57272	0.57825	0.06319	0.06434	0.7512	0.75049	0.47604	0.4748	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25435	25435	SRR25868973	SRX21590432	SRS18768005	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.	T1Hh2	strain:AB wild type\|age:6 24hpf\|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 55960\|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:1\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hh2 S197	T1Hh2 S197	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	T1Hh2_S197_L002_R1_001.fastq.gz T1Hh2_S197_L002_R2_001.fastq.gz	fastq fastq	6387795600.0	21292652.0	T1Hh2 S197 L002 R1 001.fastq.gz	0:150 1:150	A:1680625940;C:1435118036;G:1640302670;T:1631616836;N:132118	150	150	1680625940	1435118036	1640302670	1631616836	132118	SRX21590432	SRS18768005	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62371	0.63132	0.05956	0.06039	0.74014	0.73868	0.47123	0.47075	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25436	25436	SRR25868974	SRX21590431	SRS18768004	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.	T1Hh1	strain:AB wild type\|age:6 24hpf\|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 55959\|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:1\|dose:15.355903608562938\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hh1 S17	T1Hh1 S17	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	T1Hh1_S17_L001_R1_001.fastq.gz T1Hh1_S17_L001_R2_001.fastq.gz	fastq fastq	6049552200.0	20165174.0	T1Hh1 S17 L001 R1 001.fastq.gz	0:150 1:150	A:1582015084;C:1352466278;G:1586556106;T:1528389233;N:125499	150	150	1582015084	1352466278	1586556106	1528389233	125499	SRX21590431	SRS18768004	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66156	0.66516	0.08381	0.08543	0.74403	0.74535	0.48607	0.4876	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25437	25437	SRR25868975	SRX21590430	SRS18768003	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.	T1Hg5	strain:AB wild type\|age:6 24hpf\|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 55958\|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:1\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hg5 S196	T1Hg5 S196	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	T1Hg5_S196_L002_R1_001.fastq.gz T1Hg5_S196_L002_R2_001.fastq.gz	fastq fastq	2969169900.0	9897233.0	T1Hg5 S196 L002 R1 001.fastq.gz	0:150 1:150	A:771265530;C:670039228;G:783041882;T:744761956;N:61304	150	150	771265530	670039228	783041882	744761956	61304	SRX21590430	SRS18768003	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60729	0.61493	0.06034	0.06188	0.73931	0.7388	0.47362	0.46325	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25438	25438	SRR25868976	SRX21590429	SRS18768002	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.	T1Hg4	strain:AB wild type\|age:6 24hpf\|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 55957\|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:1\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hg4 S68	T1Hg4 S68	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	T1Hg4_S68_L001_R1_001.fastq.gz T1Hg4_S68_L001_R2_001.fastq.gz	fastq fastq	5904343800.0	19681146.0	T1Hg4 S68 L001 R1 001.fastq.gz	0:150 1:150	A:1568116381;C:1310726276;G:1506752686;T:1518621399;N:127058	150	150	1568116381	1310726276	1506752686	1518621399	127058	SRX21590429	SRS18768002	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63628	0.64678	0.07594	0.07861	0.73486	0.73393	0.47827	0.47888	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25439	25439	SRR25868977	SRX21590428	SRS18768001	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.	T1Hg3	strain:AB wild type\|age:6 24hpf\|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 55956\|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:1\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hg3 S144	T1Hg3 S144	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	T1Hg3_S144_L002_R1_001.fastq.gz T1Hg3_S144_L002_R2_001.fastq.gz	fastq fastq	6534743100.0	21782477.0	T1Hg3 S144 L002 R1 001.fastq.gz	0:150 1:150	A:1726508099;C:1490518830;G:1638045710;T:1679623196;N:47265	150	150	1726508099	1490518830	1638045710	1679623196	47265	SRX21590428	SRS18768001	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.70728	0.71532	0.08417	0.08568	0.73247	0.73229	0.47603	0.47596	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25440	25440	SRR25868978	SRX21590427	SRS18767999	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.	T1Hg2	strain:AB wild type\|age:6 24hpf\|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 55955\|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:1\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hg2 S395	T1Hg2 S395	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	T1Hg2_S395_L004_R1_001.fastq.gz T1Hg2_S395_L004_R2_001.fastq.gz	fastq fastq	8551327200.0	28504424.0	T1Hg2 S395 L004 R1 001.fastq.gz	0:150 1:150	A:2245159697;C:1916200716;G:2228219656;T:2161673806;N:73325	150	150	2245159697	1916200716	2228219656	2161673806	73325	SRX21590427	SRS18767999	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60722	0.61314	0.0758	0.07738	0.74621	0.74574	0.47977	0.48218	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25441	25441	SRR25868979	SRX21590426	SRS18768000	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.	T1Hg1	strain:AB wild type\|age:6 24hpf\|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 55954\|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:1\|dose:49.49145359392848\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hg1 S16	T1Hg1 S16	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	T1Hg1_S16_L001_R1_001.fastq.gz T1Hg1_S16_L001_R2_001.fastq.gz	fastq fastq	8955028200.0	29850094.0	T1Hg1 S16 L001 R1 001.fastq.gz	0:150 1:150	A:2393828618;C:1981188691;G:2249789051;T:2330035340;N:186500	150	150	2393828618	1981188691	2249789051	2330035340	186500	SRX21590426	SRS18768000	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65935	0.66533	0.07846	0.08043	0.73348	0.73255	0.47	0.47482	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25442	25442	SRR25868980	SRX21590425	SRS18767998	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.	T1VBh8	strain:AB wild type\|age:6 24hpf\|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 55819\|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:1\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep16\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VBh8 S20	T1VBh8 S20	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	T1VBh8_S20_L001_R1_001.fastq.gz T1VBh8_S20_L001_R2_001.fastq.gz	fastq fastq	6064035300.0	20213451.0	T1VBh8 S20 L001 R1 001.fastq.gz	0:150 1:150	A:1561097089;C:1390203789;G:1566818214;T:1545874613;N:41595	150	150	1561097089	1390203789	1566818214	1545874613	41595	SRX21590425	SRS18767998	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62447	0.63168	0.06708	0.06924	0.74083	0.73945	0.47006	0.46573	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25443	25443	SRR25868981	SRX21590424	SRS18767997	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.	T1Hf5	strain:AB wild type\|age:6 24hpf\|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 55953\|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:1\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hf5 S15	T1Hf5 S15	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	T1Hf5_S15_L001_R1_001.fastq.gz T1Hf5_S15_L001_R2_001.fastq.gz	fastq fastq	6052159200.0	20173864.0	T1Hf5 S15 L001 R1 001.fastq.gz	0:150 1:150	A:1621205734;C:1315559782;G:1572284216;T:1542987318;N:122150	150	150	1621205734	1315559782	1572284216	1542987318	122150	SRX21590424	SRS18767997	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61939	0.62504	0.06837	0.07109	0.73821	0.7389	0.47477	0.47658	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25444	25444	SRR25868982	SRX21590423	SRS18767996	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.	T1Hf4	strain:AB wild type\|age:6 24hpf\|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 55952\|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:1\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hf4 S67	T1Hf4 S67	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	T1Hf4_S67_L001_R1_001.fastq.gz T1Hf4_S67_L001_R2_001.fastq.gz	fastq fastq	5449258800.0	18164196.0	T1Hf4 S67 L001 R1 001.fastq.gz	0:150 1:150	A:1424014438;C:1223501372;G:1436442982;T:1365181873;N:118135	150	150	1424014438	1223501372	1436442982	1365181873	118135	SRX21590423	SRS18767996	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61165	0.62075	0.06357	0.06536	0.73908	0.73868	0.47593	0.47651	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25445	25445	SRR25868983	SRX21590422	SRS18767995	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.	T1Hf3	strain:AB wild type\|age:6 24hpf\|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 55951\|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:1\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hf3 S394	T1Hf3 S394	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	T1Hf3_S394_L004_R1_001.fastq.gz T1Hf3_S394_L004_R2_001.fastq.gz	fastq fastq	7232101200.0	24107004.0	T1Hf3 S394 L004 R1 001.fastq.gz	0:150 1:150	A:1894135875;C:1623660249;G:1903093804;T:1811147682;N:63590	150	150	1894135875	1623660249	1903093804	1811147682	63590	SRX21590422	SRS18767995	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60773	0.61297	0.05724	0.05891	0.74057	0.74057	0.47014	0.46754	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25446	25446	SRR25868984	SRX21590421	SRS18767992	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.	T1Hf2	strain:AB wild type\|age:6 24hpf\|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 55950\|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:1\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hf2 S143	T1Hf2 S143	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	T1Hf2_S143_L002_R1_001.fastq.gz T1Hf2_S143_L002_R2_001.fastq.gz	fastq fastq	7033257300.0	23444191.0	T1Hf2 S143 L002 R1 001.fastq.gz	0:150 1:150	A:1821704834;C:1591775557;G:1848826391;T:1770898370;N:52148	150	150	1821704834	1591775557	1848826391	1770898370	52148	SRX21590421	SRS18767992	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59947	0.60641	0.05753	0.05892	0.74531	0.74452	0.47144	0.47528	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25447	25447	SRR25868985	SRX21590420	SRS18767994	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.	T1Hf1	strain:AB wild type\|age:6 24hpf\|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 55949\|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:1\|dose:191.2535433776785\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hf1 S195	T1Hf1 S195	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	T1Hf1_S195_L002_R1_001.fastq.gz T1Hf1_S195_L002_R2_001.fastq.gz	fastq fastq	2862946800.0	9543156.0	T1Hf1 S195 L002 R1 001.fastq.gz	0:150 1:150	A:751165058;C:639523105;G:754580961;T:717618340;N:59336	150	150	751165058	639523105	754580961	717618340	59336	SRX21590420	SRS18767994	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60944	0.61653	0.05708	0.05948	0.74477	0.74477	0.47818	0.47943	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25448	25448	SRR25868986	SRX21590419	SRS18767989	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.	T1He5	strain:AB wild type\|age:6 24hpf\|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 55948\|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:1\|dose:577.9573054842787\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1He5 S393	T1He5 S393	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	T1He5_S393_L004_R1_001.fastq.gz T1He5_S393_L004_R2_001.fastq.gz	fastq fastq	7130028900.0	23766763.0	T1He5 S393 L004 R1 001.fastq.gz	0:150 1:150	A:1880847071;C:1594278633;G:1844288124;T:1810554636;N:60436	150	150	1880847071	1594278633	1844288124	1810554636	60436	SRX21590419	SRS18767989	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62014	0.627	0.05601	0.05779	0.73614	0.73608	0.46211	0.46154	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25449	25449	SRR25868987	SRX21590418	SRS18767990	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.	T1He4	strain:AB wild type\|age:6 24hpf\|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 55947\|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:1\|dose:577.9573054842787\|dose units:ug/L\|treatment:PFHxS CAS 355 46 4\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1He4 S142	T1He4 S142	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	T1He4_S142_L002_R1_001.fastq.gz T1He4_S142_L002_R2_001.fastq.gz	fastq fastq	6234150900.0	20780503.0	T1He4 S142 L002 R1 001.fastq.gz	0:150 1:150	A:1636685518;C:1429222586;G:1554474804;T:1613721955;N:46037	150	150	1636685518	1429222586	1554474804	1613721955	46037	SRX21590418	SRS18767990	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.73543	0.74718	0.07205	0.07454	0.7273	0.72685	0.47559	0.46518	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25498	25498	SRR25869036	SRX21590369	SRS18767944	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.	T2Sh3	strain:AB wild type\|age:6 48hpf\|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 56581\|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:2\|dose:7.38905609893065\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sh3 S16	T2Sh3 S16	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	T2Sh3_S16_L001_R1_001.fastq.gz T2Sh3_S16_L001_R2_001.fastq.gz	fastq fastq	5141284500.0	17137615.0	T2Sh3 S16 L001 R1 001.fastq.gz	0:150 1:150	A:1342165699;C:1164772238;G:1348671691;T:1285561325;N:113547	150	150	1342165699	1164772238	1348671691	1285561325	113547	SRX21590369	SRS18767944	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63282	0.64214	0.07465	0.07703	0.73182	0.73034	0.46906	0.47118	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25499	25499	SRR25869037	SRX21590368	SRS18767942	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.	T2Sh2	strain:AB wild type\|age:6 48hpf\|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 56580\|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:2\|dose:7\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sh2 S30	T2Sh2 S30	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	T2Sh2_S30_L003_R1_001.fastq.gz T2Sh2_S30_L003_R2_001.fastq.gz	fastq fastq	4710576000.0	15701920.0	T2Sh2 S30 L003 R1 001.fastq.gz	0:150 1:150	A:1231447711;C:1054164938;G:1265281849;T:1159607410;N:74092	150	150	1231447711	1054164938	1265281849	1159607410	74092	SRX21590368	SRS18767942	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.597	0.60177	0.07162	0.07295	0.74067	0.74018	0.47462	0.47184	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25500	25500	SRR25869038	SRX21590367	SRS18767943	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.	T2Sh1	strain:AB wild type\|age:6 48hpf\|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 56579\|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:2\|dose:7.38905609893065\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sh1 S141	T2Sh1 S141	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	T2Sh1_S141_L002_R1_001.fastq.gz T2Sh1_S141_L002_R2_001.fastq.gz	fastq fastq	4731084000.0	15770280.0	T2Sh1 S141 L002 R1 001.fastq.gz	0:150 1:150	A:1229124645;C:1062713495;G:1247663350;T:1191486143;N:96367	150	150	1229124645	1062713495	1247663350	1191486143	96367	SRX21590367	SRS18767943	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58042	0.58413	0.06093	0.06251	0.73892	0.73921	0.4629	0.46495	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25501	25501	SRR25869039	SRX21590366	SRS18767938	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.	T2Sg5	strain:AB wild type\|age:6 48hpf\|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 56578\|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:2\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sg5 S35	T2Sg5 S35	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	T2Sg5_S35_L001_R1_001.fastq.gz T2Sg5_S35_L001_R2_001.fastq.gz	fastq fastq	6143656800.0	20478856.0	T2Sg5 S35 L001 R1 001.fastq.gz	0:150 1:150	A:1643370769;C:1349615937;G:1584643365;T:1565987611;N:39118	150	150	1643370769	1349615937	1584643365	1565987611	39118	SRX21590366	SRS18767938	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60443	0.61069	0.08032	0.08227	0.73377	0.73357	0.46758	0.47069	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25502	25502	SRR25869040	SRX21590365	SRS18767939	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.	T2Sg4	strain:AB wild type\|age:6 48hpf\|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 56577\|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:2\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sg4 S288	T2Sg4 S288	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	T2Sg4_S288_L003_R1_001.fastq.gz T2Sg4_S288_L003_R2_001.fastq.gz	fastq fastq	7409879100.0	24699597.0	T2Sg4 S288 L003 R1 001.fastq.gz	0:150 1:150	A:1946670188;C:1675533512;G:1917674101;T:1869935115;N:66184	150	150	1946670188	1675533512	1917674101	1869935115	66184	SRX21590365	SRS18767939	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60869	0.61323	0.06751	0.06908	0.73689	0.73622	0.45619	0.46785	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25503	25503	SRR25869041	SRX21590364	SRS18767937	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.	T2Sg3	strain:AB wild type\|age:6 48hpf\|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 56576\|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:2\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sg3 S15	T2Sg3 S15	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	T2Sg3_S15_L001_R1_001.fastq.gz T2Sg3_S15_L001_R2_001.fastq.gz	fastq fastq	5239073100.0	17463577.0	T2Sg3 S15 L001 R1 001.fastq.gz	0:150 1:150	A:1379722690;C:1181303683;G:1374778240;T:1303154891;N:113596	150	150	1379722690	1181303683	1374778240	1303154891	113596	SRX21590364	SRS18767937	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63808	0.64599	0.07645	0.07851	0.73318	0.73221	0.44792	0.45264	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25504	25504	SRR25869042	SRX21590363	SRS18767936	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.	T2Sg2	strain:AB wild type\|age:6 48hpf\|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 56575\|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:2\|dose:33\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sg2 S29	T2Sg2 S29	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	T2Sg2_S29_L003_R1_001.fastq.gz T2Sg2_S29_L003_R2_001.fastq.gz	fastq fastq	5058284400.0	16860948.0	T2Sg2 S29 L003 R1 001.fastq.gz	0:150 1:150	A:1313100894;C:1133750528;G:1353544052;T:1257811020;N:77906	150	150	1313100894	1133750528	1353544052	1257811020	77906	SRX21590363	SRS18767936	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57926	0.58315	0.06534	0.06602	0.73691	0.73701	0.47106	0.46922	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25505	25505	SRR25869043	SRX21590362	SRS18767932	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.	T2Sg1	strain:AB wild type\|age:6 48hpf\|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 56574\|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:2\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sg1 S140	T2Sg1 S140	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	T2Sg1_S140_L002_R1_001.fastq.gz T2Sg1_S140_L002_R2_001.fastq.gz	fastq fastq	5038464300.0	16794881.0	T2Sg1 S140 L002 R1 001.fastq.gz	0:150 1:150	A:1329825058;C:1123244212;G:1321774466;T:1263515521;N:105043	150	150	1329825058	1123244212	1321774466	1263515521	105043	SRX21590362	SRS18767932	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58977	0.59658	0.07696	0.07919	0.73841	0.7377	0.45861	0.46116	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25507	25507	SRR25869045	SRX21590360	SRS18767935	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.	T2Sf5	strain:AB wild type\|age:6 48hpf\|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 56573\|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:2\|dose:113\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sf5 S28	T2Sf5 S28	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	T2Sf5_S28_L003_R1_001.fastq.gz T2Sf5_S28_L003_R2_001.fastq.gz	fastq fastq	3919176600.0	13063922.0	T2Sf5 S28 L003 R1 001.fastq.gz	0:150 1:150	A:1033847568;C:871570794;G:1007214290;T:1006481959;N:61989	150	150	1033847568	871570794	1007214290	1006481959	61989	SRX21590360	SRS18767935	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60206	0.60991	0.08076	0.08256	0.73813	0.7374	0.467	0.46879	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25508	25508	SRR25869046	SRX21590359	SRS18767931	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.	T2Sf4	strain:AB wild type\|age:6 48hpf\|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 56572\|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:2\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sf4 S14	T2Sf4 S14	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	T2Sf4_S14_L001_R1_001.fastq.gz T2Sf4_S14_L001_R2_001.fastq.gz	fastq fastq	4694962500.0	15649875.0	T2Sf4 S14 L001 R1 001.fastq.gz	0:150 1:150	A:1222248711;C:1072885170;G:1214979205;T:1184748320;N:101094	150	150	1222248711	1072885170	1214979205	1184748320	101094	SRX21590359	SRS18767931	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63234	0.64255	0.07471	0.07693	0.73505	0.73397	0.45838	0.45255	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25509	25509	SRR25869047	SRX21590358	SRS18767933	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.	T2Sf3	strain:AB wild type\|age:6 48hpf\|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 56571\|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:2\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sf3 S34	T2Sf3 S34	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	T2Sf3_S34_L001_R1_001.fastq.gz T2Sf3_S34_L001_R2_001.fastq.gz	fastq fastq	5936646000.0	19788820.0	T2Sf3 S34 L001 R1 001.fastq.gz	0:150 1:150	A:1556614754;C:1332453724;G:1550610231;T:1496926009;N:41282	150	150	1556614754	1332453724	1550610231	1496926009	41282	SRX21590358	SRS18767933	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6088	0.61517	0.07512	0.07732	0.73472	0.73367	0.45517	0.45519	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25510	25510	SRR25869048	SRX21590357	SRS18767930	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.	T2Sf2	strain:AB wild type\|age:6 48hpf\|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 56570\|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:2\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sf2 S287	T2Sf2 S287	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	T2Sf2_S287_L003_R1_001.fastq.gz T2Sf2_S287_L003_R2_001.fastq.gz	fastq fastq	10332497700.0	34441659.0	T2Sf2 S287 L003 R1 001.fastq.gz	0:150 1:150	A:2715756008;C:2302443888;G:2741358929;T:2572869981;N:68894	150	150	2715756008	2302443888	2741358929	2572869981	68894	SRX21590357	SRS18767930	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.55516	0.55945	0.06381	0.06492	0.7431	0.74209	0.45944	0.46222	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25511	25511	SRR25869049	SRX21590356	SRS18767929	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.	T2Sf1	strain:AB wild type\|age:6 48hpf\|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 56569\|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:2\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Sf1 S139	T2Sf1 S139	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	T2Sf1_S139_L002_R1_001.fastq.gz T2Sf1_S139_L002_R2_001.fastq.gz	fastq fastq	5546563200.0	18488544.0	T2Sf1 S139 L002 R1 001.fastq.gz	0:150 1:150	A:1451253400;C:1238761792;G:1471968475;T:1384462374;N:117159	150	150	1451253400	1238761792	1471968475	1384462374	117159	SRX21590356	SRS18767929	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59035	0.59671	0.06117	0.06309	0.74117	0.73992	0.44737	0.44737	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25512	25512	SRR25869050	SRX21590355	SRS18767928	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.	T2Se5	strain:AB wild type\|age:6 48hpf\|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 56568\|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:2\|dose:506\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Se5 S27	T2Se5 S27	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	T2Se5_S27_L003_R1_001.fastq.gz T2Se5_S27_L003_R2_001.fastq.gz	fastq fastq	3862803300.0	12876011.0	T2Se5 S27 L003 R1 001.fastq.gz	0:150 1:150	A:1004437313;C:864913078;G:1016883629;T:976509384;N:59896	150	150	1004437313	864913078	1016883629	976509384	59896	SRX21590355	SRS18767928	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59031	0.59649	0.07792	0.0792	0.73914	0.73795	0.45496	0.45822	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25513	25513	SRR25869051	SRX21590354	SRS18767927	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.	T2Se4	strain:AB wild type\|age:6 48hpf\|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 56567\|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:2\|dose:506.1838787429168\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T2Se4 S13	T2Se4 S13	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	T2Se4_S13_L001_R1_001.fastq.gz T2Se4_S13_L001_R2_001.fastq.gz	fastq fastq	5169663300.0	17232211.0	T2Se4 S13 L001 R1 001.fastq.gz	0:150 1:150	A:1365540616;C:1164709355;G:1334484585;T:1304816781;N:111963	150	150	1365540616	1164709355	1334484585	1304816781	111963	SRX21590354	SRS18767927	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66846	0.6761	0.07739	0.07962	0.72549	0.7249	0.44845	0.44884	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25514	25514	SRR25869052	SRX21590353	SRS18767926	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.	T1Sb2 rep	strain:AB wild type\|age:6 24hpf\|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 56508\|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:1\|dose:20825\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb2 rep S100	T1Sb2 rep S100	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	T1Sb2_rep_S100_L003_R1_001.fastq.gz T1Sb2_rep_S100_L003_R2_001.fastq.gz	fastq fastq	3519926400.0	11733088.0	T1Sb2 rep S100 L003 R1 001.fastq.gz	0:150 1:150	A:905459774;C:793533536;G:948747587;T:872130003;N:55500	150	150	905459774	793533536	948747587	872130003	55500	SRX21590353	SRS18767926	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.5595	0.56771	0.05767	0.05893	0.75103	0.75014	0.46945	0.47006	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25515	25515	SRR25869053	SRX21590352	SRS18767925	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.	T1Sb2	strain:AB wild type\|age:6 24hpf\|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 56507\|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:1\|dose:20824.80284992842\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb2 S127	T1Sb2 S127	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	T1Sb2_S127_L002_R1_001.fastq.gz T1Sb2_S127_L002_R2_001.fastq.gz	fastq fastq	3214709400.0	10715698.0	T1Sb2 S127 L002 R1 001.fastq.gz	0:150 1:150	A:827728741;C:725270926;G:863536486;T:798107574;N:65673	150	150	827728741	725270926	863536486	798107574	65673	SRX21590352	SRS18767925	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56774	0.57587	0.05969	0.06033	0.7484	0.74744	0.46527	0.47143	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25516	25516	SRR25869054	SRX21590351	SRS18767924	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.	T1Sb1	strain:AB wild type\|age:6 24hpf\|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 56506\|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:1\|dose:20824.80284992842\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb1 S265	T1Sb1 S265	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	T1Sb1_S265_L003_R1_001.fastq.gz T1Sb1_S265_L003_R2_001.fastq.gz	fastq fastq	8435057100.0	28116857.0	T1Sb1 S265 L003 R1 001.fastq.gz	0:150 1:150	A:2252274212;C:1860526389;G:2160715403;T:2161466433;N:74663	150	150	2252274212	1860526389	2160715403	2161466433	74663	SRX21590351	SRS18767924	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63069	0.63834	0.07115	0.07339	0.73588	0.73584	0.47419	0.46845	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25517	25517	SRR25869055	SRX21590350	SRS18767923	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.	T1Sa5	strain:AB wild type\|age:6 24hpf\|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 56505\|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:1\|dose:74406.60546411345\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sa5 S264	T1Sa5 S264	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	T1Sa5_S264_L003_R1_001.fastq.gz T1Sa5_S264_L003_R2_001.fastq.gz	fastq fastq	7644515700.0	25481719.0	T1Sa5 S264 L003 R1 001.fastq.gz	0:150 1:150	A:2026252471;C:1658421442;G:2011222542;T:1948552767;N:66478	150	150	2026252471	1658421442	2011222542	1948552767	66478	SRX21590350	SRS18767923	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58158	0.58525	0.0633	0.06508	0.74663	0.74759	0.47815	0.47494	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25518	25518	SRR25869056	SRX21590349	SRS18767922	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.	T1Sa4	strain:AB wild type\|age:6 24hpf\|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 56504\|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:1\|dose:74406.60546411345\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sa4 S1	T1Sa4 S1	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	T1Sa4_S1_L001_R1_001.fastq.gz T1Sa4_S1_L001_R2_001.fastq.gz	fastq fastq	5700786600.0	19002622.0	T1Sa4 S1 L001 R1 001.fastq.gz	0:150 1:150	A:1534507666;C:1234898401;G:1469466526;T:1461787186;N:126821	150	150	1534507666	1234898401	1469466526	1461787186	126821	SRX21590349	SRS18767922	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60678	0.61548	0.06574	0.06752	0.74296	0.74176	0.47335	0.47457	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25520	25520	SRR25869058	SRX21590347	SRS18767920	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.	T1VAh1	strain:AB wild type\|age:6 24hpf\|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 55811\|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:1\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep8\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VAh1 S272	T1VAh1 S272	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	T1VAh1_S272_L003_R1_001.fastq.gz T1VAh1_S272_L003_R2_001.fastq.gz	fastq fastq	7177785900.0	23925953.0	T1VAh1 S272 L003 R1 001.fastq.gz	0:150 1:150	A:1847561052;C:1653957526;G:1896135400;T:1780068981;N:62941	150	150	1847561052	1653957526	1896135400	1780068981	62941	SRX21590347	SRS18767920	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63432	0.63996	0.08898	0.09021	0.75179	0.75077	0.48991	0.47251	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25521	25521	SRR25869059	SRX21590346	SRS18767919	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.	T1Sa3	strain:AB wild type\|age:6 24hpf\|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 56503\|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:1\|dose:74407\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sa3 S15	T1Sa3 S15	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	T1Sa3_S15_L003_R1_001.fastq.gz T1Sa3_S15_L003_R2_001.fastq.gz	fastq fastq	4640742000.0	15469140.0	T1Sa3 S15 L003 R1 001.fastq.gz	0:150 1:150	A:1187978301;C:1058732375;G:1249170739;T:1144790501;N:70084	150	150	1187978301	1058732375	1249170739	1144790501	70084	SRX21590346	SRS18767919	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56158	0.56633	0.06598	0.06646	0.7498	0.7489	0.48146	0.4795	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25522	25522	SRR25869060	SRX21590345	SRS18767916	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.	T1Sa2	strain:AB wild type\|age:6 24hpf\|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 56502\|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:1\|dose:74406.60546411345\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sa2 S126	T1Sa2 S126	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	T1Sa2_S126_L002_R1_001.fastq.gz T1Sa2_S126_L002_R2_001.fastq.gz	fastq fastq	3002044500.0	10006815.0	T1Sa2 S126 L002 R1 001.fastq.gz	0:150 1:150	A:801885075;C:661843312;G:773023778;T:765229680;N:62655	150	150	801885075	661843312	773023778	765229680	62655	SRX21590345	SRS18767916	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60048	0.61032	0.06552	0.06773	0.73787	0.73797	0.46503	0.46733	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25523	25523	SRR25869061	SRX21590344	SRS18767915	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.	T1Sa1	strain:AB wild type\|age:6 24hpf\|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 56501\|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:1\|dose:74406.60546411345\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sa1 S11	T1Sa1 S11	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	T1Sa1_S11_L001_R1_001.fastq.gz T1Sa1_S11_L001_R2_001.fastq.gz	fastq fastq	8499248700.0	28330829.0	T1Sa1 S11 L001 R1 001.fastq.gz	0:150 1:150	A:2204199806;C:1933220854;G:2209369401;T:2152400861;N:57778	150	150	2204199806	1933220854	2209369401	2152400861	57778	SRX21590344	SRS18767915	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65181	0.65294	0.07072	0.071	0.73904	0.7401	0.47139	0.47121	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Pharyngula	Embryo	Trunk	Surface Structure
25586	25586	SRR25868813	SRX21590281	SRS18767854	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.	T3Sh2	strain:AB wild type\|age:24 48hpf\|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 56623\|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:3\|dose:7.38905609893065\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sh2 S54	T3Sh2 S54	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	T3Sh2_S54_L001_R1_001.fastq.gz T3Sh2_S54_L001_R2_001.fastq.gz	fastq fastq	6582103800.0	21940346.0	T3Sh2 S54 L001 R1 001.fastq.gz	0:150 1:150	A:1726133946;C:1480517305;G:1719005880;T:1656401769;N:44900	150	150	1726133946	1480517305	1719005880	1656401769	44900	SRX21590281	SRS18767854	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64092	0.64705	0.08687	0.08952	0.73675	0.73643	0.48212	0.4802	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25587	25587	SRR25868814	SRX21590280	SRS18767852	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.	T3Sh1	strain:AB wild type\|age:24 48hpf\|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 56622\|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:3\|dose:7\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sh1 S307	T3Sh1 S307	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	T3Sh1_S307_L003_R1_001.fastq.gz T3Sh1_S307_L003_R2_001.fastq.gz	fastq fastq	7697145000.0	25657150.0	T3Sh1 S307 L003 R1 001.fastq.gz	0:150 1:150	A:2044494130;C:1708203812;G:1976603106;T:1967776849;N:67103	150	150	2044494130	1708203812	1976603106	1967776849	67103	SRX21590280	SRS18767852	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60675	0.60813	0.06673	0.06792	0.7363	0.73781	0.47123	0.474	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25588	25588	SRR25868815	SRX21590279	SRS18767851	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.	T3Sg5	strain:AB wild type\|age:24 48hpf\|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 56621\|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:3\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sg5 S148	T3Sg5 S148	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	T3Sg5_S148_L002_R1_001.fastq.gz T3Sg5_S148_L002_R2_001.fastq.gz	fastq fastq	4253529300.0	14178431.0	T3Sg5 S148 L002 R1 001.fastq.gz	0:150 1:150	A:1103458117;C:982514807;G:1096043214;T:1071426736;N:86426	150	150	1103458117	982514807	1096043214	1071426736	86426	SRX21590279	SRS18767851	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.70148	0.71378	0.10131	0.10459	0.73708	0.73553	0.49603	0.49834	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25589	25589	SRR25868816	SRX21590278	SRS18767850	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.	T3Sg4	strain:AB wild type\|age:24 48hpf\|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 56620\|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:3\|dose:33\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sg4 S37	T3Sg4 S37	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	T3Sg4_S37_L003_R1_001.fastq.gz T3Sg4_S37_L003_R2_001.fastq.gz	fastq fastq	4321313100.0	14404377.0	T3Sg4 S37 L003 R1 001.fastq.gz	0:150 1:150	A:1096679729;C:998982656;G:1180179058;T:1045406529;N:65128	150	150	1096679729	998982656	1180179058	1045406529	65128	SRX21590278	SRS18767850	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57857	0.58241	0.07725	0.0773	0.75144	0.75047	0.47526	0.47085	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25590	25590	SRR25868817	SRX21590277	SRS18767856	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.	T3Sg3	strain:AB wild type\|age:24 48hpf\|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 56619\|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:3\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sg3 S53	T3Sg3 S53	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	T3Sg3_S53_L001_R1_001.fastq.gz T3Sg3_S53_L001_R2_001.fastq.gz	fastq fastq	5506286400.0	18354288.0	T3Sg3 S53 L001 R1 001.fastq.gz	0:150 1:150	A:1400407854;C:1255730505;G:1497661808;T:1352449189;N:37044	150	150	1400407854	1255730505	1497661808	1352449189	37044	SRX21590277	SRS18767856	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6024	0.60515	0.05941	0.06008	0.7445	0.74367	0.456	0.45959	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25591	25591	SRR25868818	SRX21590276	SRS18767849	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.	T3Sg2	strain:AB wild type\|age:24 48hpf\|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 56618\|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:3\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sg2 S306	T3Sg2 S306	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	T3Sg2_S306_L003_R1_001.fastq.gz T3Sg2_S306_L003_R2_001.fastq.gz	fastq fastq	8869185900.0	29563953.0	T3Sg2 S306 L003 R1 001.fastq.gz	0:150 1:150	A:2365409182;C:1954925886;G:2253316872;T:2295454781;N:79179	150	150	2365409182	1954925886	2253316872	2295454781	79179	SRX21590276	SRS18767849	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60222	0.60674	0.07367	0.07577	0.7389	0.73866	0.46772	0.4694	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25592	25592	SRR25868819	SRX21590275	SRS18767848	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.	T3Sg1	strain:AB wild type\|age:24 48hpf\|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 56617\|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:3\|dose:32.76628203789861\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sg1 S23	T3Sg1 S23	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	T3Sg1_S23_L001_R1_001.fastq.gz T3Sg1_S23_L001_R2_001.fastq.gz	fastq fastq	5804202000.0	19347340.0	T3Sg1 S23 L001 R1 001.fastq.gz	0:150 1:150	A:1520091710;C:1302024534;G:1494612710;T:1487344670;N:128376	150	150	1520091710	1302024534	1494612710	1487344670	128376	SRX21590275	SRS18767848	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60029	0.60942	0.07333	0.07563	0.74148	0.74091	0.46608	0.46947	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25593	25593	SRR25868820	SRX21590274	SRS18767845	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.	T3Sf5	strain:AB wild type\|age:24 48hpf\|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 56616\|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:3\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep6\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf5 S147	T3Sf5 S147	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	T3Sf5_S147_L002_R1_001.fastq.gz T3Sf5_S147_L002_R2_001.fastq.gz	fastq fastq	5018207700.0	16727359.0	T3Sf5 S147 L002 R1 001.fastq.gz	0:150 1:150	A:1320208034;C:1137103908;G:1278511622;T:1282281881;N:102255	150	150	1320208034	1137103908	1278511622	1282281881	102255	SRX21590274	SRS18767845	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.69291	0.70432	0.07868	0.081	0.72661	0.72519	0.44983	0.45032	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25594	25594	SRR25868821	SRX21590273	SRS18767843	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.	T3Sf4	strain:AB wild type\|age:24 48hpf\|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 56615\|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:3\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf4 S305	T3Sf4 S305	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	T3Sf4_S305_L003_R1_001.fastq.gz T3Sf4_S305_L003_R2_001.fastq.gz	fastq fastq	5755618500.0	19185395.0	T3Sf4 S305 L003 R1 001.fastq.gz	0:150 1:150	A:1523049402;C:1284306673;G:1507197068;T:1441013676;N:51681	150	150	1523049402	1284306673	1507197068	1441013676	51681	SRX21590273	SRS18767843	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59623	0.6024	0.04996	0.05185	0.73758	0.73724	0.44677	0.44219	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25595	25595	SRR25868822	SRX21590272	SRS18767844	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.	T3Sf3 rep	strain:AB wild type\|age:24 48hpf\|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 56614\|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:3\|dose:113\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf3 rep S97	T3Sf3 rep S97	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	T3Sf3_rep_S97_L003_R1_001.fastq.gz T3Sf3_rep_S97_L003_R2_001.fastq.gz	fastq fastq	4273080300.0	14243601.0	T3Sf3 rep S97 L003 R1 001.fastq.gz	0:150 1:150	A:1105965090;C:965177319;G:1154319246;T:1047552490;N:66155	150	150	1105965090	965177319	1154319246	1047552490	66155	SRX21590272	SRS18767844	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58656	0.59145	0.05817	0.05931	0.74596	0.74558	0.45848	0.45992	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25597	25597	SRR25868824	SRX21590270	SRS18767847	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.	T3Sf3	strain:AB wild type\|age:24 48hpf\|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 56613\|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:3\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf3 S52	T3Sf3 S52	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	T3Sf3_S52_L001_R1_001.fastq.gz T3Sf3_S52_L001_R2_001.fastq.gz	fastq fastq	6038188800.0	20127296.0	T3Sf3 S52 L001 R1 001.fastq.gz	0:150 1:150	A:1553512544;C:1377515439;G:1618604484;T:1488514475;N:41858	150	150	1553512544	1377515439	1618604484	1488514475	41858	SRX21590270	SRS18767847	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62512	0.63026	0.06147	0.06276	0.74079	0.74008	0.46696	0.46598	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25598	25598	SRR25868825	SRX21590269	SRS18767842	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.	T3Sf2	strain:AB wild type\|age:24 48hpf\|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 56612\|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:3\|dose:113\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf2 S36	T3Sf2 S36	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	T3Sf2_S36_L003_R1_001.fastq.gz T3Sf2_S36_L003_R2_001.fastq.gz	fastq fastq	4569037200.0	15230124.0	T3Sf2 S36 L003 R1 001.fastq.gz	0:150 1:150	A:1171936028;C:1056304715;G:1203431494;T:1137296229;N:68734	150	150	1171936028	1056304715	1203431494	1137296229	68734	SRX21590269	SRS18767842	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60907	0.61495	0.07823	0.07937	0.73996	0.73921	0.46665	0.47422	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25599	25599	SRR25868826	SRX21590268	SRS18767840	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.	T3Sf1	strain:AB wild type\|age:24 48hpf\|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 56611\|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:3\|dose:112.65161463773616\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sf1 S22	T3Sf1 S22	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	T3Sf1_S22_L001_R1_001.fastq.gz T3Sf1_S22_L001_R2_001.fastq.gz	fastq fastq	6418545000.0	21395150.0	T3Sf1 S22 L001 R1 001.fastq.gz	0:150 1:150	A:1715836818;C:1410285882;G:1678828276;T:1613451757;N:142267	150	150	1715836818	1410285882	1678828276	1613451757	142267	SRX21590268	SRS18767840	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61685	0.62434	0.06736	0.06913	0.7372	0.73734	0.46485	0.46229	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25600	25600	SRR25868827	SRX21590267	SRS18767839	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.	T3Se5	strain:AB wild type\|age:24 48hpf\|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 56610\|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:3\|dose:506\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Se5 S35	T3Se5 S35	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	T3Se5_S35_L003_R1_001.fastq.gz T3Se5_S35_L003_R2_001.fastq.gz	fastq fastq	4603582800.0	15345276.0	T3Se5 S35 L003 R1 001.fastq.gz	0:150 1:150	A:1206542376;C:1035789405;G:1199882419;T:1161297792;N:70808	150	150	1206542376	1035789405	1199882419	1161297792	70808	SRX21590267	SRS18767839	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61848	0.62535	0.07524	0.07737	0.73425	0.73361	0.46944	0.46671	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25601	25601	SRR25868828	SRX21590266	SRS18767838	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.	T3Sc1	strain:AB wild type\|age:24 48hpf\|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 56595\|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:3\|dose:6385.595311090952\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sc1 S144	T3Sc1 S144	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	T3Sc1_S144_L002_R1_001.fastq.gz T3Sc1_S144_L002_R2_001.fastq.gz	fastq fastq	4637934300.0	15459781.0	T3Sc1 S144 L002 R1 001.fastq.gz	0:150 1:150	A:1214353581;C:1056409986;G:1183797101;T:1183279388;N:94244	150	150	1214353581	1056409986	1183797101	1183279388	94244	SRX21590266	SRS18767838	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.7042	0.71602	0.07455	0.07794	0.72433	0.72403	0.46477	0.46292	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25602	25602	SRR25868829	SRX21590265	SRS18767841	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.	T3Sb5	strain:AB wild type\|age:24 48hpf\|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 56594\|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:3\|dose:20824.80284992842\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sb5 S143	T3Sb5 S143	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	T3Sb5_S143_L002_R1_001.fastq.gz T3Sb5_S143_L002_R2_001.fastq.gz	fastq fastq	3972004200.0	13240014.0	T3Sb5 S143 L002 R1 001.fastq.gz	0:150 1:150	A:1033928165;C:912309294;G:1031084609;T:994601104;N:81028	150	150	1033928165	912309294	1031084609	994601104	81028	SRX21590265	SRS18767841	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67426	0.68473	0.06174	0.06376	0.72687	0.72555	0.46059	0.45349	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25604	25604	SRR25868831	SRX21590263	SRS18767837	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.	T3Sb4	strain:AB wild type\|age:24 48hpf\|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 56593\|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:3\|dose:20825\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sb4 S32	T3Sb4 S32	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	T3Sb4_S32_L003_R1_001.fastq.gz T3Sb4_S32_L003_R2_001.fastq.gz	fastq fastq	4171132200.0	13903774.0	T3Sb4 S32 L003 R1 001.fastq.gz	0:150 1:150	A:1079556601;C:953574771;G:1107436338;T:1030500058;N:64432	150	150	1079556601	953574771	1107436338	1030500058	64432	SRX21590263	SRS18767837	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63433	0.64012	0.0607	0.06183	0.73561	0.73462	0.45188	0.45005	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25605	25605	SRR25868832	SRX21590262	SRS18767834	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.	T3Sb3	strain:AB wild type\|age:24 48hpf\|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 56592\|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:3\|dose:20824.80284992842\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sb3 S48	T3Sb3 S48	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	T3Sb3_S48_L001_R1_001.fastq.gz T3Sb3_S48_L001_R2_001.fastq.gz	fastq fastq	6817527000.0	22725090.0	T3Sb3 S48 L001 R1 001.fastq.gz	0:150 1:150	A:1771861770;C:1540486858;G:1833554922;T:1671575980;N:47470	150	150	1771861770	1540486858	1833554922	1671575980	47470	SRX21590262	SRS18767834	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61374	0.61843	0.06189	0.06329	0.73793	0.73667	0.45589	0.45157	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure
25606	25606	SRR25868833	SRX21590261	SRS18767833	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.	T3Sb2	strain:AB wild type\|age:24 48hpf\|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 56591\|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:3\|dose:20824.80284992842\|dose units:ug/L\|treatment:PFOS CAS 1763 21 1\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T3Sb2 S301	T3Sb2 S301	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	T3Sb2_S301_L003_R1_001.fastq.gz T3Sb2_S301_L003_R2_001.fastq.gz	fastq fastq	9844025100.0	32813417.0	T3Sb2 S301 L003 R1 001.fastq.gz	0:150 1:150	A:2606652952;C:2199628657;G:2530535919;T:2507119942;N:87630	150	150	2606652952	2199628657	2530535919	2507119942	87630	SRX21590261	SRS18767833	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64109	0.64791	0.07943	0.08202	0.73643	0.73584	0.46618	0.46317	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Hatching	Embryo	Trunk	Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;