metadata: run_metadata: 228 rows where devstage_curation = "Pharyngula" and tissue

228 rows where devstage_curation = "Pharyngula" 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
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
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
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
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
25617	25617	SRR25868844	SRX21590250	SRS18767822	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.	T1Se2	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 56523\|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:506.1838787429168\|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	T1Se2 S268	T1Se2 S268	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	T1Se2_S268_L003_R1_001.fastq.gz T1Se2_S268_L003_R2_001.fastq.gz	fastq fastq	7441881000.0	24806270.0	T1Se2 S268 L003 R1 001.fastq.gz	0:150 1:150	A:1951632139;C:1644032654;G:1956340778;T:1889811043;N:64386	150	150	1951632139	1644032654	1956340778	1889811043	64386	SRX21590250	SRS18767822	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.55018	0.55503	0.04777	0.0494	0.74945	0.74894	0.47071	0.4695	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
25618	25618	SRR25868845	SRX21590249	SRS18767820	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.	T1Se1	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 56522\|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:506.1838787429168\|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	T1Se1 S130	T1Se1 S130	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	T1Se1_S130_L002_R1_001.fastq.gz T1Se1_S130_L002_R2_001.fastq.gz	fastq fastq	3625618500.0	12085395.0	T1Se1 S130 L002 R1 001.fastq.gz	0:150 1:150	A:956104688;C:795109904;G:965843919;T:908484676;N:75313	150	150	956104688	795109904	965843919	908484676	75313	SRX21590249	SRS18767820	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.54282	0.55213	0.05118	0.05252	0.7502	0.74897	0.4784	0.47341	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
25619	25619	SRR25868846	SRX21590248	SRS18767823	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.	T1Sd5	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 56521\|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:1639\|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	T1Sd5 S18	T1Sd5 S18	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	T1Sd5_S18_L003_R1_001.fastq.gz T1Sd5_S18_L003_R2_001.fastq.gz	fastq fastq	3949711800.0	13165706.0	T1Sd5 S18 L003 R1 001.fastq.gz	0:150 1:150	A:1029012663;C:877817037;G:1075222253;T:967599531;N:60316	150	150	1029012663	877817037	1075222253	967599531	60316	SRX21590248	SRS18767823	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57015	0.57344	0.05704	0.05758	0.75146	0.7513	0.48719	0.48701	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
25620	25620	SRR25868847	SRX21590247	SRS18767821	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.	T1Sd4	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 56520\|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:1638.931853855588\|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	T1Sd4 S267	T1Sd4 S267	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	T1Sd4_S267_L003_R1_001.fastq.gz T1Sd4_S267_L003_R2_001.fastq.gz	fastq fastq	9002395500.0	30007985.0	T1Sd4 S267 L003 R1 001.fastq.gz	0:150 1:150	A:2346740724;C:2016593522;G:2383401737;T:2255581344;N:78173	150	150	2346740724	2016593522	2383401737	2255581344	78173	SRX21590247	SRS18767821	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56469	0.56875	0.05049	0.0522	0.74734	0.74661	0.47557	0.47531	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
25621	25621	SRR25868848	SRX21590246	SRS18767819	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.	T1Sd3	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 56519\|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:1638.931853855588\|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	T1Sd3 S14	T1Sd3 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	T1Sd3_S14_L001_R1_001.fastq.gz T1Sd3_S14_L001_R2_001.fastq.gz	fastq fastq	6539823600.0	21799412.0	T1Sd3 S14 L001 R1 001.fastq.gz	0:150 1:150	A:1730364321;C:1465242561;G:1688972867;T:1655199121;N:44730	150	150	1730364321	1465242561	1688972867	1655199121	44730	SRX21590246	SRS18767819	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66709	0.67323	0.06928	0.0715	0.73655	0.73622	0.46708	0.47193	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
25622	25622	SRR25868849	SRX21590245	SRS18767817	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.	T1Sd2	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 56518\|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:1638.931853855588\|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	T1Sd2 S4	T1Sd2 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	T1Sd2_S4_L001_R1_001.fastq.gz T1Sd2_S4_L001_R2_001.fastq.gz	fastq fastq	5364693900.0	17882313.0	T1Sd2 S4 L001 R1 001.fastq.gz	0:150 1:150	A:1374211847;C:1224520183;G:1438779702;T:1327062975;N:119193	150	150	1374211847	1224520183	1438779702	1327062975	119193	SRX21590245	SRS18767817	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60138	0.60911	0.06127	0.0627	0.74383	0.74345	0.47872	0.47895	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
25623	25623	SRR25868850	SRX21590244	SRS18767816	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.	T1Sd1	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 56517\|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:1638.931853855588\|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	T1Sd1 S129	T1Sd1 S129	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	T1Sd1_S129_L002_R1_001.fastq.gz T1Sd1_S129_L002_R2_001.fastq.gz	fastq fastq	5757648300.0	19192161.0	T1Sd1 S129 L002 R1 001.fastq.gz	0:150 1:150	A:1515825620;C:1278196477;G:1506252467;T:1457252650;N:121086	150	150	1515825620	1278196477	1506252467	1457252650	121086	SRX21590244	SRS18767816	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57707	0.58423	0.05955	0.06102	0.74673	0.74558	0.47024	0.47361	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
25624	25624	SRR25868851	SRX21590243	SRS18767818	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.	T1Sc9	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 56516\|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:6386\|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	T1Sc9 S17	T1Sc9 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	T1Sc9_S17_L003_R1_001.fastq.gz T1Sc9_S17_L003_R2_001.fastq.gz	fastq fastq	4201398000.0	14004660.0	T1Sc9 S17 L003 R1 001.fastq.gz	0:150 1:150	A:1101497644;C:939920232;G:1105018635;T:1054896126;N:65363	150	150	1101497644	939920232	1105018635	1054896126	65363	SRX21590243	SRS18767818	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59103	0.59651	0.09069	0.09153	0.7555	0.75467	0.4977	0.49746	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
25625	25625	SRR25868852	SRX21590242	SRS18767814	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.	T1Sc5	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 56515\|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:6385.595311090952\|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	T1Sc5 S266	T1Sc5 S266	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	T1Sc5_S266_L003_R1_001.fastq.gz T1Sc5_S266_L003_R2_001.fastq.gz	fastq fastq	5453324100.0	18177747.0	T1Sc5 S266 L003 R1 001.fastq.gz	0:150 1:150	A:1445741979;C:1187804467;G:1441261305;T:1378467507;N:48842	150	150	1445741979	1187804467	1441261305	1378467507	48842	SRX21590242	SRS18767814	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.5709	0.57618	0.0556	0.057	0.74899	0.74858	0.46753	0.47414	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
25626	25626	SRR25868853	SRX21590241	SRS18767815	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.	T1Sc3	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 56514\|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:6385.595311090952\|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	T1Sc3 S3	T1Sc3 S3	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	T1Sc3_S3_L001_R1_001.fastq.gz T1Sc3_S3_L001_R2_001.fastq.gz	fastq fastq	6545163600.0	21817212.0	T1Sc3 S3 L001 R1 001.fastq.gz	0:150 1:150	A:1702041515;C:1475860236;G:1755688831;T:1611430698;N:142320	150	150	1702041515	1475860236	1755688831	1611430698	142320	SRX21590241	SRS18767815	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59369	0.60128	0.08875	0.09047	0.74915	0.7485	0.48685	0.48982	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
25628	25628	SRR25868855	SRX21590239	SRS18767811	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.	T1Sc2	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 56513\|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:6385.595311090952\|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	T1Sc2 S13	T1Sc2 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	T1Sc2_S13_L001_R1_001.fastq.gz T1Sc2_S13_L001_R2_001.fastq.gz	fastq fastq	6788321100.0	22627737.0	T1Sc2 S13 L001 R1 001.fastq.gz	0:150 1:150	A:1801894099;C:1518997683;G:1745230590;T:1722153705;N:45023	150	150	1801894099	1518997683	1745230590	1722153705	45023	SRX21590239	SRS18767811	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66763	0.67211	0.06944	0.07042	0.73768	0.73789	0.47721	0.48255	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
25629	25629	SRR25868856	SRX21590238	SRS18767812	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.	T1Sc1	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 56512\|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: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	T1Sc1 S128	T1Sc1 S128	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	T1Sc1_S128_L002_R1_001.fastq.gz T1Sc1_S128_L002_R2_001.fastq.gz	fastq fastq	3180347100.0	10601157.0	T1Sc1 S128 L002 R1 001.fastq.gz	0:150 1:150	A:845385003;C:699920964;G:836882088;T:798092292;N:66753	150	150	845385003	699920964	836882088	798092292	66753	SRX21590238	SRS18767812	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58311	0.59062	0.06545	0.06698	0.74477	0.74373	0.48017	0.47977	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
25630	25630	SRR25868857	SRX21590237	SRS18767809	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.	T1Sb5	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 56511\|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:rep6\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb5 S12	T1Sb5 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	T1Sb5_S12_L001_R1_001.fastq.gz T1Sb5_S12_L001_R2_001.fastq.gz	fastq fastq	5621277900.0	18737593.0	T1Sb5 S12 L001 R1 001.fastq.gz	0:150 1:150	A:1455842307;C:1283018160;G:1484906907;T:1397475146;N:35380	150	150	1455842307	1283018160	1484906907	1397475146	35380	SRX21590237	SRS18767809	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65251	0.65773	0.06017	0.06186	0.73807	0.73791	0.46723	0.46005	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
25631	25631	SRR25868858	SRX21590236	SRS18767810	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.	T1Sb4	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 56510\|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:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb4 S16	T1Sb4 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	T1Sb4_S16_L003_R1_001.fastq.gz T1Sb4_S16_L003_R2_001.fastq.gz	fastq fastq	4768317900.0	15894393.0	T1Sb4 S16 L003 R1 001.fastq.gz	0:150 1:150	A:1267572230;C:1045859899;G:1241216327;T:1213595527;N:73917	150	150	1267572230	1045859899	1241216327	1213595527	73917	SRX21590236	SRS18767810	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58172	0.59031	0.07228	0.07368	0.74649	0.74584	0.48869	0.4881	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
25632	25632	SRR25868859	SRX21590235	SRS18767808	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.	T1Sb3	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 56509\|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:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOS CAS 1763 21 1	T1Sb3 S2	T1Sb3 S2	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	T1Sb3_S2_L001_R1_001.fastq.gz T1Sb3_S2_L001_R2_001.fastq.gz	fastq fastq	4842392100.0	16141307.0	T1Sb3 S2 L001 R1 001.fastq.gz	0:150 1:150	A:1256980104;C:1093688837;G:1297096640;T:1194522742;N:103777	150	150	1256980104	1093688837	1297096640	1194522742	103777	SRX21590235	SRS18767808	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60182	0.61014	0.06482	0.0661	0.74207	0.74059	0.46478	0.46842	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
25681	25681	SRR25868908	SRX21590186	SRS18767760	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.	T1Ad4 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 56234\|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\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep6\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad4 rep S13	T1Ad4 rep 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	T1Ad4_rep_S13_L003_R1_001.fastq.gz T1Ad4_rep_S13_L003_R2_001.fastq.gz	fastq fastq	4205499000.0	14018330.0	T1Ad4 rep S13 L003 R1 001.fastq.gz	0:150 1:150	A:1109227219;C:936940584;G:1089540742;T:1069725054;N:65401	150	150	1109227219	936940584	1089540742	1069725054	65401	SRX21590186	SRS18767760	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62097	0.62975	0.06186	0.06403	0.73949	0.73864	0.47164	0.47234	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
25683	25683	SRR25868910	SRX21590184	SRS18767758	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.	T1Ad4	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 56233\|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:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad4 S384	T1Ad4 S384	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	T1Ad4_S384_L004_R1_001.fastq.gz T1Ad4_S384_L004_R2_001.fastq.gz	fastq fastq	6103193400.0	20343978.0	T1Ad4 S384 L004 R1 001.fastq.gz	0:150 1:150	A:1602496883;C:1374351246;G:1568595969;T:1557696926;N:52376	150	150	1602496883	1374351246	1568595969	1557696926	52376	SRX21590184	SRS18767758	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65676	0.66504	0.06455	0.06663	0.73476	0.73462	0.45941	0.4593	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
25684	25684	SRR25868911	SRX21590183	SRS18767754	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.	T1Ad3	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 56232\|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:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad3 S133	T1Ad3 S133	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	T1Ad3_S133_L002_R1_001.fastq.gz T1Ad3_S133_L002_R2_001.fastq.gz	fastq fastq	6140372400.0	20467908.0	T1Ad3 S133 L002 R1 001.fastq.gz	0:150 1:150	A:1571702270;C:1424082100;G:1614347633;T:1530195492;N:44905	150	150	1571702270	1424082100	1614347633	1530195492	44905	SRX21590183	SRS18767754	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65618	0.66143	0.06174	0.06289	0.7405	0.7399	0.47586	0.47653	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
25685	25685	SRR25868912	SRX21590182	SRS18767753	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.	T1Ad2 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 56231\|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:rep3\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad2 rep S166	T1Ad2 rep S166	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	T1Ad2_rep_S166_L002_R1_001.fastq.gz T1Ad2_rep_S166_L002_R2_001.fastq.gz	fastq fastq	4313391900.0	14377973.0	T1Ad2 rep S166 L002 R1 001.fastq.gz	0:150 1:150	A:1138392930;C:974045863;G:1087901945;T:1112960481;N:90681	150	150	1138392930	974045863	1087901945	1112960481	90681	SRX21590182	SRS18767753	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.68743	0.69832	0.06657	0.06851	0.72691	0.72567	0.46162	0.45753	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
25686	25686	SRR25868913	SRX21590181	SRS18767756	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.	T1Ad2	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 56230\|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:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ad2 S5	T1Ad2 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	T1Ad2_S5_L001_R1_001.fastq.gz T1Ad2_S5_L001_R2_001.fastq.gz	fastq fastq	4948268100.0	16494227.0	T1Ad2 S5 L001 R1 001.fastq.gz	0:150 1:150	A:1285312941;C:1091084971;G:1364887191;T:1206880728;N:102269	150	150	1285312941	1091084971	1364887191	1206880728	102269	SRX21590181	SRS18767756	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.53643	0.53873	0.05027	0.05117	0.75237	0.7529	0.45652	0.4537	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
25755	25755	SRR25868671	SRX21590112	SRS18767685	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.	T1VAd7	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 55807\|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:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VAd7 S18	T1VAd7 S18	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	T1VAd7_S18_L001_R1_001.fastq.gz T1VAd7_S18_L001_R2_001.fastq.gz	fastq fastq	7861843500.0	26206145.0	T1VAd7 S18 L001 R1 001.fastq.gz	0:150 1:150	A:2045655756;C:1731767561;G:2171834700;T:1912424506;N:160977	150	150	2045655756	1731767561	2171834700	1912424506	160977	SRX21590112	SRS18767685	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.54367	0.54323	0.06395	0.06426	0.76108	0.76209	0.48415	0.49151	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
25815	25815	SRR25868731	SRX21590052	SRS18767623	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.	T1Hh5	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 55963\|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:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hh5 S145	T1Hh5 S145	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	T1Hh5_S145_L002_R1_001.fastq.gz T1Hh5_S145_L002_R2_001.fastq.gz	fastq fastq	6986923200.0	23289744.0	T1Hh5 S145 L002 R1 001.fastq.gz	0:150 1:150	A:1834059922;C:1534248093;G:1841122493;T:1777441756;N:50936	150	150	1834059922	1534248093	1841122493	1777441756	50936	SRX21590052	SRS18767623	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56319	0.56835	0.06933	0.07069	0.74828	0.74801	0.47209	0.4743	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
25816	25816	SRR25868732	SRX21590051	SRS18767625	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.	T1Hh4	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 55962\|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:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1Hh4 S69	T1Hh4 S69	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	T1Hh4_S69_L001_R1_001.fastq.gz T1Hh4_S69_L001_R2_001.fastq.gz	fastq fastq	6305670300.0	21018901.0	T1Hh4 S69 L001 R1 001.fastq.gz	0:150 1:150	A:1619897091;C:1446777452;G:1677848221;T:1561008621;N:138915	150	150	1619897091	1446777452	1677848221	1561008621	138915	SRX21590051	SRS18767625	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61432	0.62284	0.06334	0.06495	0.74391	0.743	0.47017	0.47108	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
25817	25817	SRR25868733	SRX21590050	SRS18767624	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.	T1Hb4	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 55932\|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:23250.92046210953\|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	T1Hb4 S139	T1Hb4 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	T1Hb4_S139_L002_R1_001.fastq.gz T1Hb4_S139_L002_R2_001.fastq.gz	fastq fastq	8225910600.0	27419702.0	T1Hb4 S139 L002 R1 001.fastq.gz	0:150 1:150	A:2164471279;C:1849008818;G:2087070711;T:2125298952;N:60840	150	150	2164471279	1849008818	2087070711	2125298952	60840	SRX21590050	SRS18767624	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64028	0.64929	0.07013	0.07271	0.73369	0.73352	0.48071	0.48071	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
25818	25818	SRR25868734	SRX21590049	SRS18767621	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.	T1Hb3	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 55931\|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:23250.92046210953\|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	T1Hb3 S63	T1Hb3 S63	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	T1Hb3_S63_L001_R1_001.fastq.gz T1Hb3_S63_L001_R2_001.fastq.gz	fastq fastq	5227150800.0	17423836.0	T1Hb3 S63 L001 R1 001.fastq.gz	0:150 1:150	A:1374795586;C:1183859665;G:1331168322;T:1337226215;N:101012	150	150	1374795586	1183859665	1331168322	1337226215	101012	SRX21590049	SRS18767621	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65042	0.66157	0.06807	0.06964	0.7347	0.73367	0.46857	0.47011	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
25819	25819	SRR25868735	SRX21590048	SRS18767620	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.	T1Hb2	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 55930\|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:23250.92046210953\|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	T1Hb2 S390	T1Hb2 S390	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	T1Hb2_S390_L004_R1_001.fastq.gz T1Hb2_S390_L004_R2_001.fastq.gz	fastq fastq	6444459900.0	21481533.0	T1Hb2 S390 L004 R1 001.fastq.gz	0:150 1:150	A:1686754722;C:1446995923;G:1670245765;T:1640416506;N:46984	150	150	1686754722	1446995923	1670245765	1640416506	46984	SRX21590048	SRS18767620	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61578	0.62348	0.06763	0.06985	0.74219	0.74117	0.46785	0.47724	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
25820	25820	SRR25868736	SRX21590047	SRS18767619	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.	T1Hb1	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 55929\|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:23250.92046210953\|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	T1Hb1 S191	T1Hb1 S191	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	T1Hb1_S191_L002_R1_001.fastq.gz T1Hb1_S191_L002_R2_001.fastq.gz	fastq fastq	4341720300.0	14472401.0	T1Hb1 S191 L002 R1 001.fastq.gz	0:150 1:150	A:1134109003;C:969064273;G:1153117872;T:1085337890;N:91262	150	150	1134109003	969064273	1153117872	1085337890	91262	SRX21590047	SRS18767619	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60424	0.61137	0.06165	0.0627	0.74231	0.74225	0.47136	0.47828	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
25821	25821	SRR25868737	SRX21590046	SRS18767622	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.	T1Ha5	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 55928\|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:65394.92924766719\|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	T1Ha5 S10	T1Ha5 S10	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	T1Ha5_S10_L001_R1_001.fastq.gz T1Ha5_S10_L001_R2_001.fastq.gz	fastq fastq	5906690700.0	19688969.0	T1Ha5 S10 L001 R1 001.fastq.gz	0:150 1:150	A:1560749780;C:1309202878;G:1531739760;T:1504880565;N:117717	150	150	1560749780	1309202878	1531739760	1504880565	117717	SRX21590046	SRS18767622	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64799	0.65439	0.06478	0.06674	0.73283	0.73223	0.47272	0.47319	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
25822	25822	SRR25868738	SRX21590045	SRS18767617	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.	T1Ha4	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 55927\|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:65394.92924766719\|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	T1Ha4 S138	T1Ha4 S138	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	T1Ha4_S138_L002_R1_001.fastq.gz T1Ha4_S138_L002_R2_001.fastq.gz	fastq fastq	8836329300.0	29454431.0	T1Ha4 S138 L002 R1 001.fastq.gz	0:150 1:150	A:2296305968;C:1996706043;G:2345685145;T:2197567766;N:64378	150	150	2296305968	1996706043	2345685145	2197567766	64378	SRX21590045	SRS18767617	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62781	0.63389	0.06648	0.0676	0.74166	0.74197	0.48378	0.48089	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
25823	25823	SRR25868739	SRX21590044	SRS18767618	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.	T1Ha3	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 55926\|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:65394.92924766719\|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	T1Ha3 S62	T1Ha3 S62	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	T1Ha3_S62_L001_R1_001.fastq.gz T1Ha3_S62_L001_R2_001.fastq.gz	fastq fastq	4839590700.0	16131969.0	T1Ha3 S62 L001 R1 001.fastq.gz	0:150 1:150	A:1243509017;C:1112322997;G:1275370493;T:1208284399;N:103794	150	150	1243509017	1112322997	1275370493	1208284399	103794	SRX21590044	SRS18767618	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60112	0.6094	0.0588	0.05972	0.74355	0.74259	0.45368	0.45233	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
25824	25824	SRR25868740	SRX21590043	SRS18767616	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.	T1Ha2	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 55925\|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:65394.92924766719\|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	T1Ha2 S389	T1Ha2 S389	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	T1Ha2_S389_L004_R1_001.fastq.gz T1Ha2_S389_L004_R2_001.fastq.gz	fastq fastq	6527693700.0	21758979.0	T1Ha2 S389 L004 R1 001.fastq.gz	0:150 1:150	A:1647609591;C:1506635174;G:1771166929;T:1602227299;N:54707	150	150	1647609591	1506635174	1771166929	1602227299	54707	SRX21590043	SRS18767616	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57656	0.57686	0.07545	0.07642	0.75659	0.75877	0.50157	0.50172	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
25825	25825	SRR25868741	SRX21590042	SRS18767615	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.	T1Ha1	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 55924\|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:65394.92924766719\|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	T1Ha1 S190	T1Ha1 S190	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	T1Ha1_S190_L002_R1_001.fastq.gz T1Ha1_S190_L002_R2_001.fastq.gz	fastq fastq	5126714400.0	17089048.0	T1Ha1 S190 L002 R1 001.fastq.gz	0:150 1:150	A:1334459848;C:1150765246;G:1363440485;T:1277943979;N:104842	150	150	1334459848	1150765246	1363440485	1277943979	104842	SRX21590042	SRS18767615	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58539	0.592	0.06392	0.06481	0.74594	0.74483	0.47453	0.47398	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
25826	25826	SRR25868742	SRX21590041	SRS18767614	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.	T1VBe5	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 55816\|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:rep13\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VBe5 S398	T1VBe5 S398	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	T1VBe5_S398_L004_R1_001.fastq.gz T1VBe5_S398_L004_R2_001.fastq.gz	fastq fastq	8563247400.0	28544158.0	T1VBe5 S398 L004 R1 001.fastq.gz	0:150 1:150	A:2247947986;C:1900099790;G:2240731765;T:2174395375;N:72484	150	150	2247947986	1900099790	2240731765	2174395375	72484	SRX21590041	SRS18767614	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66269	0.67122	0.05731	0.0594	0.72949	0.72868	0.46768	0.46973	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
25893	25893	SRR25868465	SRX21589974	SRS18767548	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.	T1VAf6	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 55809\|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:rep6\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VAf6 S91	T1VAf6 S91	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	T1VAf6_S91_L003_R1_001.fastq.gz T1VAf6_S91_L003_R2_001.fastq.gz	fastq fastq	5239674000.0	17465580.0	T1VAf6 S91 L003 R1 001.fastq.gz	0:150 1:150	A:1361622694;C:1174410988;G:1409014962;T:1294557880;N:67476	150	150	1361622694	1174410988	1409014962	1294557880	67476	SRX21589974	SRS18767548	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59522	0.60119	0.05954	0.06114	0.74334	0.74328	0.48954	0.49022	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
25913	25913	SRR25868485	SRX21589954	SRS18767527	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.	T1Ah5	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 56256\|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:15.620747522178164\|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	T1Ah5 S388	T1Ah5 S388	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	T1Ah5_S388_L004_R1_001.fastq.gz T1Ah5_S388_L004_R2_001.fastq.gz	fastq fastq	7612622400.0	25375408.0	T1Ah5 S388 L004 R1 001.fastq.gz	0:150 1:150	A:1954328891;C:1755973662;G:2018504113;T:1883749488;N:66246	150	150	1954328891	1755973662	2018504113	1883749488	66246	SRX21589954	SRS18767527	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61002	0.61607	0.05996	0.06067	0.74418	0.74347	0.48012	0.469	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
25914	25914	SRR25868486	SRX21589953	SRS18767526	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.	T1Ah3	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 56255\|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:15.620747522178164\|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	T1Ah3 S9	T1Ah3 S9	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	T1Ah3_S9_L001_R1_001.fastq.gz T1Ah3_S9_L001_R2_001.fastq.gz	fastq fastq	3714228300.0	12380761.0	T1Ah3 S9 L001 R1 001.fastq.gz	0:150 1:150	A:980004722;C:811072838;G:988293959;T:934781610;N:75171	150	150	980004722	811072838	988293959	934781610	75171	SRX21589953	SRS18767526	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56295	0.55387	0.04783	0.04775	0.74578	0.74744	0.47797	0.4741	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
25915	25915	SRR25868487	SRX21589952	SRS18767524	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.	T1Ah2	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 56254\|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:15.620747522178164\|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	T1Ah2 S263	T1Ah2 S263	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	T1Ah2_S263_L003_R1_001.fastq.gz T1Ah2_S263_L003_R2_001.fastq.gz	fastq fastq	6673069800.0	22243566.0	T1Ah2 S263 L003 R1 001.fastq.gz	0:150 1:150	A:1736552223;C:1489994862;G:1796288186;T:1650177674;N:56855	150	150	1736552223	1489994862	1796288186	1650177674	56855	SRX21589952	SRS18767524	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57662	0.5689	0.06475	0.06441	0.7502	0.75175	0.48324	0.47823	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
25917	25917	SRR25868489	SRX21589950	SRS18767523	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.	T1Ah10	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 56253\|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:15.620747522178164\|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	T1Ah1 S10	T1Ah1 S10	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	T1Ah1_S10_L001_R1_001.fastq.gz T1Ah1_S10_L001_R2_001.fastq.gz	fastq fastq	8097806400.0	26992688.0	T1Ah1 S10 L001 R1 001.fastq.gz	0:150 1:150	A:2106833603;C:1810877341;G:2152324139;T:2027715616;N:55701	150	150	2106833603	1810877341	2152324139	2027715616	55701	SRX21589950	SRS18767523	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60795	0.61343	0.08293	0.08418	0.74982	0.7501	0.50417	0.49961	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
25918	25918	SRR25868490	SRX21589949	SRS18767522	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.	T1Ah1	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 56252\|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:15.620747522178164\|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	T1Ah10 S137	T1Ah10 S137	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	T1Ah10_S137_L002_R1_001.fastq.gz T1Ah10_S137_L002_R2_001.fastq.gz	fastq fastq	5634088800.0	18780296.0	T1Ah10 S137 L002 R1 001.fastq.gz	0:150 1:150	A:1469139312;C:1272261463;G:1472669312;T:1419977528;N:41185	150	150	1469139312	1272261463	1472669312	1419977528	41185	SRX21589949	SRS18767522	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65286	0.65657	0.10304	0.10532	0.74917	0.75065	0.47891	0.49578	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
25919	25919	SRR25868491	SRX21589948	SRS18767521	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.	T1Ag5	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 56251\|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:51.80051027056361\|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	T1Ag5 S9	T1Ag5 S9	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	T1Ag5_S9_L001_R1_001.fastq.gz T1Ag5_S9_L001_R2_001.fastq.gz	fastq fastq	7659987000.0	25533290.0	T1Ag5 S9 L001 R1 001.fastq.gz	0:150 1:150	A:2008451699;C:1720528767;G:1971478391;T:1959477006;N:51137	150	150	2008451699	1720528767	1971478391	1959477006	51137	SRX21589948	SRS18767521	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64233	0.65079	0.0693	0.0719	0.74101	0.74109	0.48433	0.47934	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
25920	25920	SRR25868492	SRX21589947	SRS18767520	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.	T1Ag4	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 56250\|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:51.80051027056361\|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	T1Ag4 S387	T1Ag4 S387	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	T1Ag4_S387_L004_R1_001.fastq.gz T1Ag4_S387_L004_R2_001.fastq.gz	fastq fastq	6233241000.0	20777470.0	T1Ag4 S387 L004 R1 001.fastq.gz	0:150 1:150	A:1535979865;C:1429410330;G:1784695234;T:1483101588;N:53983	150	150	1535979865	1429410330	1784695234	1483101588	53983	SRX21589947	SRS18767520	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.51507	0.51541	0.03739	0.03741	0.76708	0.76743	0.46886	0.47184	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
25921	25921	SRR25868493	SRX21589946	SRS18767517	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	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 56220\|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:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab4 S3	T1Ab4 S3	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_S3_L001_R1_001.fastq.gz T1Ab4_S3_L001_R2_001.fastq.gz	fastq fastq	2750631600.0	9168772.0	T1Ab4 S3 L001 R1 001.fastq.gz	0:150 1:150	A:711955524;C:603794720;G:752829771;T:681996414;N:55171	150	150	711955524	603794720	752829771	681996414	55171	SRX21589946	SRS18767517	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.56186	0.56717	0.05002	0.05165	0.75345	0.75351	0.46766	0.46799	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
25922	25922	SRR25868494	SRX21589945	SRS18767518	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.	T1Ab3	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 56219\|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:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab3 S131	T1Ab3 S131	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	T1Ab3_S131_L002_R1_001.fastq.gz T1Ab3_S131_L002_R2_001.fastq.gz	fastq fastq	7604892000.0	25349640.0	T1Ab3 S131 L002 R1 001.fastq.gz	0:150 1:150	A:2023196813;C:1676943563;G:1952854100;T:1951840827;N:56697	150	150	2023196813	1676943563	1952854100	1951840827	56697	SRX21589945	SRS18767518	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64192	0.64976	0.07356	0.07609	0.73843	0.7387	0.47568	0.47398	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
25923	25923	SRR25868495	SRX21589944	SRS18767519	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.	T1Ab2	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 56218\|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:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab2 S257	T1Ab2 S257	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	T1Ab2_S257_L003_R1_001.fastq.gz T1Ab2_S257_L003_R2_001.fastq.gz	fastq fastq	3333976800.0	11113256.0	T1Ab2 S257 L003 R1 001.fastq.gz	0:150 1:150	A:880636179;C:738205957;G:868887778;T:846217805;N:29081	150	150	880636179	738205957	868887778	846217805	29081	SRX21589944	SRS18767519	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.5972	0.60463	0.06447	0.06643	0.74089	0.7403	0.46994	0.47477	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
25924	25924	SRR25868496	SRX21589943	SRS18767516	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.	T1Ab1	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 56217\|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:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Ab1 S4	T1Ab1 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	T1Ab1_S4_L001_R1_001.fastq.gz T1Ab1_S4_L001_R2_001.fastq.gz	fastq fastq	9478951200.0	31596504.0	T1Ab1 S4 L001 R1 001.fastq.gz	0:150 1:150	A:2491728394;C:2069431902;G:2492653080;T:2425073269;N:64555	150	150	2491728394	2069431902	2492653080	2425073269	64555	SRX21589943	SRS18767516	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6167	0.6256	0.06631	0.06883	0.74365	0.74207	0.47966	0.47495	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
25925	25925	SRR25868497	SRX21589942	SRS18767515	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.	T1Aa5 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 56216\|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:57325.452426386364\|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	T1Aa5 rep S150	T1Aa5 rep S150	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	T1Aa5_rep_S150_L002_R1_001.fastq.gz T1Aa5_rep_S150_L002_R2_001.fastq.gz	fastq fastq	2436598800.0	8121996.0	T1Aa5 rep S150 L002 R1 001.fastq.gz	0:150 1:150	A:646155432;C:548294764;G:621739142;T:620358333;N:51129	150	150	646155432	548294764	621739142	620358333	51129	SRX21589942	SRS18767515	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67587	0.68453	0.06644	0.06826	0.73334	0.73212	0.46065	0.45516	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
25926	25926	SRR25868498	SRX21589941	SRS18767514	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.	T1Aa5	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 56215\|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:57325.452426386364\|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	T1Aa5 S2	T1Aa5 S2	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	T1Aa5_S2_L001_R1_001.fastq.gz T1Aa5_S2_L001_R2_001.fastq.gz	fastq fastq	3668883600.0	12229612.0	T1Aa5 S2 L001 R1 001.fastq.gz	0:150 1:150	A:898970934;C:812403866;G:1085417249;T:872025728;N:65823	150	150	898970934	812403866	1085417249	872025728	65823	SRX21589941	SRS18767514	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.49809	0.4992	0.04804	0.04837	0.7595	0.75952	0.46742	0.46717	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
25927	25927	SRR25868499	SRX21589940	SRS18767513	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.	T1Aa4	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 56214\|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:57325.452426386364\|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	T1Aa4 S3	T1Aa4 S3	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	T1Aa4_S3_L001_R1_001.fastq.gz T1Aa4_S3_L001_R2_001.fastq.gz	fastq fastq	7412916300.0	24709721.0	T1Aa4 S3 L001 R1 001.fastq.gz	0:150 1:150	A:1963532151;C:1603811626;G:1999685529;T:1845836931;N:50063	150	150	1963532151	1603811626	1999685529	1845836931	50063	SRX21589940	SRS18767513	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58427	0.58879	0.06168	0.06353	0.74373	0.74308	0.47337	0.47496	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
25929	25929	SRR25868501	SRX21589938	SRS18767512	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.	T1Aa3	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 56213\|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:57325.452426386364\|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	T1Aa3 S381	T1Aa3 S381	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	T1Aa3_S381_L004_R1_001.fastq.gz T1Aa3_S381_L004_R2_001.fastq.gz	fastq fastq	6713599200.0	22378664.0	T1Aa3 S381 L004 R1 001.fastq.gz	0:150 1:150	A:1736279042;C:1530016738;G:1763661148;T:1683583946;N:58326	150	150	1736279042	1530016738	1763661148	1683583946	58326	SRX21589938	SRS18767512	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62704	0.63412	0.05192	0.05306	0.73959	0.73852	0.47493	0.47927	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
25930	25930	SRR25868502	SRX21589937	SRS18767509	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.	T1Aa2	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 56212\|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:57325.452426386364\|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	T1Aa2 S256	T1Aa2 S256	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	T1Aa2_S256_L003_R1_001.fastq.gz T1Aa2_S256_L003_R2_001.fastq.gz	fastq fastq	5544345900.0	18481153.0	T1Aa2 S256 L003 R1 001.fastq.gz	0:150 1:150	A:1411236510;C:1266320173;G:1498720987;T:1368023921;N:44309	150	150	1411236510	1266320173	1498720987	1368023921	44309	SRX21589937	SRS18767509	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57112	0.57441	0.05066	0.05139	0.75085	0.75059	0.47333	0.46188	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
25931	25931	SRR25868503	SRX21589936	SRS18767510	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.	T1Aa1 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 56211\|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:57325\|dose units:ug/L\|treatment:PFOA CAS 45285 51 6\|replicate ID:rep2\|repeat sample:Yes\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFOA CAS 45285 51 6	T1Aa1 rep S1	T1Aa1 rep 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	T1Aa1_rep_S1_L003_R1_001.fastq.gz T1Aa1_rep_S1_L003_R2_001.fastq.gz	fastq fastq	3660774900.0	12202583.0	T1Aa1 rep S1 L003 R1 001.fastq.gz	0:150 1:150	A:962893037;C:809341182;G:968344221;T:920139882;N:56578	150	150	962893037	809341182	968344221	920139882	56578	SRX21589936	SRS18767510	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.5871	0.59351	0.06352	0.06471	0.74357	0.74263	0.47688	0.47393	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
25932	25932	SRR25868504	SRX21589935	SRS18767508	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.	T1Aa1	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 56210\|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:57325.452426386364\|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	T1Aa1 S130	T1Aa1 S130	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	T1Aa1_S130_L002_R1_001.fastq.gz T1Aa1_S130_L002_R2_001.fastq.gz	fastq fastq	5151921900.0	17173073.0	T1Aa1 S130 L002 R1 001.fastq.gz	0:150 1:150	A:1351756222;C:1151515923;G:1345290600;T:1303321020;N:38135	150	150	1351756222	1151515923	1345290600	1303321020	38135	SRX21589935	SRS18767508	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62899	0.63521	0.06738	0.06863	0.73803	0.73797	0.47393	0.46895	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
25985	25985	SRR25868557	SRX21589882	SRS18767452	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.	T1He3	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 55946\|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:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1He3 S66	T1He3 S66	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	T1He3_S66_L001_R1_001.fastq.gz T1He3_S66_L001_R2_001.fastq.gz	fastq fastq	5577892200.0	18592974.0	T1He3 S66 L001 R1 001.fastq.gz	0:150 1:150	A:1456517401;C:1250275999;G:1474152816;T:1396823318;N:122666	150	150	1456517401	1250275999	1474152816	1396823318	122666	SRX21589882	SRS18767452	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.59646	0.60631	0.0677	0.07009	0.74477	0.74347	0.47783	0.47778	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
25986	25986	SRR25868558	SRX21589881	SRS18767454	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.	T1He2	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 55945\|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:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1He2 S194	T1He2 S194	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	T1He2_S194_L002_R1_001.fastq.gz T1He2_S194_L002_R2_001.fastq.gz	fastq fastq	2666998500.0	8889995.0	T1He2 S194 L002 R1 001.fastq.gz	0:150 1:150	A:695421440;C:585731847;G:739966418;T:645821736;N:57059	150	150	695421440	585731847	739966418	645821736	57059	SRX21589881	SRS18767454	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.55048	0.55347	0.04822	0.04871	0.75519	0.7544	0.46082	0.46033	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
25987	25987	SRR25868559	SRX21589880	SRS18767455	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.	T1He1	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 55944\|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:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo PFHxS CAS 355 46 4	T1He1 S14	T1He1 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	T1He1_S14_L001_R1_001.fastq.gz T1He1_S14_L001_R2_001.fastq.gz	fastq fastq	6682356900.0	22274523.0	T1He1 S14 L001 R1 001.fastq.gz	0:150 1:150	A:1782769763;C:1487760456;G:1703891377;T:1707795618;N:139686	150	150	1782769763	1487760456	1703891377	1707795618	139686	SRX21589880	SRS18767455	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61304	0.61894	0.05674	0.05873	0.73811	0.73748	0.46174	0.47056	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
25988	25988	SRR25868560	SRX21589879	SRS18767453	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.	T1VBg7	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 55818\|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:rep15\|repeat sample:No\|BioSampleModel:Model organism or animal	RNA Seq of danio rerio: whole organism embryo control	T1VBg7 S54	T1VBg7 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	T1VBg7_S54_L001_R1_001.fastq.gz T1VBg7_S54_L001_R2_001.fastq.gz	fastq fastq	5376106800.0	17920356.0	T1VBg7 S54 L001 R1 001.fastq.gz	0:150 1:150	A:1419326535;C:1202981222;G:1408792832;T:1344887367;N:118844	150	150	1419326535	1202981222	1408792832	1344887367	118844	SRX21589879	SRS18767453	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64455	0.65405	0.06495	0.06672	0.73671	0.73507	0.48368	0.4822	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
25989	25989	SRR25868561	SRX21589878	SRS18767451	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.	T1Hd5	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 55943\|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:1790.2311060034128\|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	T1Hd5 S13	T1Hd5 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	T1Hd5_S13_L001_R1_001.fastq.gz T1Hd5_S13_L001_R2_001.fastq.gz	fastq fastq	8013063000.0	26710210.0	T1Hd5 S13 L001 R1 001.fastq.gz	0:150 1:150	A:2091409302;C:1801980418;G:2096263317;T:2023243292;N:166671	150	150	2091409302	1801980418	2096263317	2023243292	166671	SRX21589878	SRS18767451	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58342	0.58684	0.06103	0.06243	0.7419	0.7419	0.47235	0.47346	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
25990	25990	SRR25868562	SRX21589877	SRS18767450	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.	T1Hd4	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 55942\|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:1790.2311060034128\|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	T1Hd4 S141	T1Hd4 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	T1Hd4_S141_L002_R1_001.fastq.gz T1Hd4_S141_L002_R2_001.fastq.gz	fastq fastq	6806155200.0	22687184.0	T1Hd4 S141 L002 R1 001.fastq.gz	0:150 1:150	A:1765858500;C:1547411307;G:1753766164;T:1739068751;N:50478	150	150	1765858500	1547411307	1753766164	1739068751	50478	SRX21589877	SRS18767450	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64253	0.65099	0.06853	0.0702	0.73724	0.73572	0.47434	0.48012	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
25991	25991	SRR25868563	SRX21589876	SRS18767449	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.	T1Hd3	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 55941\|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:1790.2311060034128\|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	T1Hd3 S193	T1Hd3 S193	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	T1Hd3_S193_L002_R1_001.fastq.gz T1Hd3_S193_L002_R2_001.fastq.gz	fastq fastq	2902996200.0	9676654.0	T1Hd3 S193 L002 R1 001.fastq.gz	0:150 1:150	A:762384792;C:650282159;G:766762045;T:723507304;N:59900	150	150	762384792	650282159	766762045	723507304	59900	SRX21589876	SRS18767449	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61969	0.62893	0.05733	0.05858	0.74144	0.73975	0.47309	0.47816	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
25992	25992	SRR25868564	SRX21589875	SRS18767448	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.	T1Hd2	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 55940\|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:1790.2311060034128\|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	T1Hd2 S65	T1Hd2 S65	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	T1Hd2_S65_L001_R1_001.fastq.gz T1Hd2_S65_L001_R2_001.fastq.gz	fastq fastq	6447102000.0	21490340.0	T1Hd2 S65 L001 R1 001.fastq.gz	0:150 1:150	A:1696150294;C:1454412155;G:1663930134;T:1632471623;N:137794	150	150	1696150294	1454412155	1663930134	1632471623	137794	SRX21589875	SRS18767448	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65352	0.66379	0.05458	0.05582	0.74046	0.73947	0.45854	0.45721	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
25993	25993	SRR25868565	SRX21589874	SRS18767447	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.	T1Hd1	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 55939\|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:1790.2311060034128\|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	T1Hd1 S392	T1Hd1 S392	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	T1Hd1_S392_L004_R1_001.fastq.gz T1Hd1_S392_L004_R2_001.fastq.gz	fastq fastq	7283875500.0	24279585.0	T1Hd1 S392 L004 R1 001.fastq.gz	0:150 1:150	A:1929428177;C:1613174093;G:1888059550;T:1853149799;N:63881	150	150	1929428177	1613174093	1888059550	1853149799	63881	SRX21589874	SRS18767447	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62135	0.62587	0.06287	0.06394	0.73624	0.73695	0.47866	0.48651	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
25994	25994	SRR25868566	SRX21589873	SRS18767446	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.	T1Hc5	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 55938\|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:7061.409807502847\|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	T1Hc5 S64	T1Hc5 S64	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	T1Hc5_S64_L001_R1_001.fastq.gz T1Hc5_S64_L001_R2_001.fastq.gz	fastq fastq	5136299700.0	17120999.0	T1Hc5 S64 L001 R1 001.fastq.gz	0:150 1:150	A:1326360832;C:1177188273;G:1346666020;T:1285972563;N:112012	150	150	1326360832	1177188273	1346666020	1285972563	112012	SRX21589873	SRS18767446	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61844	0.62831	0.06027	0.06207	0.74004	0.73894	0.47763	0.47746	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
25995	25995	SRR25868567	SRX21589872	SRS18767444	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.	T1Hc4	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 55937\|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:7061.409807502847\|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	T1Hc4 S140	T1Hc4 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	T1Hc4_S140_L002_R1_001.fastq.gz T1Hc4_S140_L002_R2_001.fastq.gz	fastq fastq	7043661000.0	23478870.0	T1Hc4 S140 L002 R1 001.fastq.gz	0:150 1:150	A:1848622791;C:1567182284;G:1855405776;T:1772397395;N:52754	150	150	1848622791	1567182284	1855405776	1772397395	52754	SRX21589872	SRS18767444	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6221	0.63073	0.06661	0.06834	0.73904	0.73681	0.46826	0.47468	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
25996	25996	SRR25868568	SRX21589871	SRS18767445	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.	T1Hc3	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 55936\|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:7061.409807502847\|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	T1Hc3 S192	T1Hc3 S192	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	T1Hc3_S192_L002_R1_001.fastq.gz T1Hc3_S192_L002_R2_001.fastq.gz	fastq fastq	3045835500.0	10152785.0	T1Hc3 S192 L002 R1 001.fastq.gz	0:150 1:150	A:811624116;C:676675011;G:761203599;T:796269425;N:63349	150	150	811624116	676675011	761203599	796269425	63349	SRX21589871	SRS18767445	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6427	0.6533	0.06898	0.07159	0.73586	0.73423	0.46627	0.46632	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
25997	25997	SRR25868569	SRX21589870	SRS18767442	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.	T1Hc2	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 55935\|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:7061.409807502847\|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	T1Hc2 S12	T1Hc2 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	T1Hc2_S12_L001_R1_001.fastq.gz T1Hc2_S12_L001_R2_001.fastq.gz	fastq fastq	6612076200.0	22040254.0	T1Hc2 S12 L001 R1 001.fastq.gz	0:150 1:150	A:1735869214;C:1465698819;G:1772711209;T:1637659272;N:137686	150	150	1735869214	1465698819	1772711209	1637659272	137686	SRX21589870	SRS18767442	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.57169	0.5742	0.04674	0.0478	0.74807	0.7483	0.48643	0.4823	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

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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");;