metadata: run_metadata: 115 rows where devstage_curation = "Multi-stage" and tissue

115 rows where devstage_curation = "Multi-stage" and tissue_curation = "Trunk"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
25713	25713	SRR25868629	SRX21590154	SRS18767725	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.				T2Ac6	strain:AB wild type\|age:6 hpf 48 hpf\|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 56271\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:2\|dose: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	T2Ac6 S150	T2Ac6 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		T2Ac6_S150_L002_R1_001.fastq.gz T2Ac6_S150_L002_R2_001.fastq.gz	fastq fastq	5789731200.0	19299104.0	T2Ac6 S150 L002 R1 001.fastq.gz	0:150 1:150	A:1481666145;C:1336138100;G:1528906855;T:1442976574;N:43526	150	150	1481666145	1336138100	1528906855	1442976574	43526	SRX21590154	SRS18767725	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63276	0.63806	0.08402	0.08572	0.74748	0.74665	0.48737	0.49137	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25718	25718	SRR25868634	SRX21590149	SRS18767721	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.				T2Ab7	strain:AB wild type\|age:6 hpf 48 hpf\|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 56266\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:2\|dose:15874.98692280121\|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	T2Ab7 S149	T2Ab7 S149	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		T2Ab7_S149_L002_R1_001.fastq.gz T2Ab7_S149_L002_R2_001.fastq.gz	fastq fastq	4855311000.0	16184370.0	T2Ab7 S149 L002 R1 001.fastq.gz	0:150 1:150	A:1261417595;C:1093785710;G:1298652014;T:1201419826;N:35855	150	150	1261417595	1093785710	1298652014	1201419826	35855	SRX21590149	SRS18767721	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61839	0.62435	0.09161	0.09367	0.74777	0.74671	0.48574	0.48713	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25833	25833	SRR25868749	SRX21590034	SRS18767606	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.				Pb12	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56783\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep9\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb12 S125	Pb12 S125	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		Pb12_S125_L001_R1_001.fastq.gz Pb12_S125_L001_R2_001.fastq.gz	fastq fastq	5732730000.0	19109100.0	Pb12 S125 L001 R1 001.fastq.gz	0:150 1:150	A:1508408271;C:1285397130;G:1474931376;T:1463868302;N:124921	150	150	1508408271	1285397130	1474931376	1463868302	124921	SRX21590034	SRS18767606	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63075	0.64107	0.09174	0.09557	0.71802	0.71701	0.49161	0.48718	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25834	25834	SRR25868750	SRX21590033	SRS18767607	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.				Pb11	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56782\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep8\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb11 S129	Pb11 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		Pb11_S129_L002_R1_001.fastq.gz Pb11_S129_L002_R2_001.fastq.gz	fastq fastq	6374115000.0	21247050.0	Pb11 S129 L002 R1 001.fastq.gz	0:150 1:150	A:1658488172;C:1446194725;G:1646655254;T:1622730483;N:46366	150	150	1658488172	1446194725	1646655254	1622730483	46366	SRX21590033	SRS18767607	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66138	0.66729	0.08662	0.09003	0.70993	0.7108	0.48394	0.48672	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25835	25835	SRR25868751	SRX21590032	SRS18767603	SRP457982	PRJNA1011844	Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds	PRJNA1011844	Other	The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature bioaccumulation in organisms and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active in addition to the toxicity endpoints that best reflect chemical hazard. In this study zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control 1uM chlorpyrifos CAS 2921 88 2 positive control and eight concentrations 0 100 uM half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1 PFOA CAS 45285 51 6 and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf 6 hpf 48 hpf 24 hpf 48 hpf 6 hpf 120 hpf 24 hpf 120 hpf 48 hpf 120 hpf 96 hpf 120 hpf to assess how common experimental design variables e.g. different exposure durations exposure at different developmental stages affect point of departure estimates.				Pa9	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56781\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep7\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa9 S254	Pa9 S254	At the end of each PFAS exposure period zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP457982		Pa9_S254_L003_R1_001.fastq.gz Pa9_S254_L003_R2_001.fastq.gz	fastq fastq	10318580700.0	34395269.0	Pa9 S254 L003 R1 001.fastq.gz	0:150 1:150	A:2688941742;C:2323349793;G:2732657504;T:2573540493;N:91168	150	150	2688941742	2323349793	2732657504	2573540493	91168	SRX21590032	SRS18767603	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.58216	0.58922	0.07708	0.07964	0.72685	0.72541	0.47803	0.47944	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25836	25836	SRR25868752	SRX21590031	SRS18767605	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.				Pa6	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56780\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep6\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa6 S77	Pa6 S77	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		Pa6_S77_L003_R1_001.fastq.gz Pa6_S77_L003_R2_001.fastq.gz	fastq fastq	4832329500.0	16107765.0	Pa6 S77 L003 R1 001.fastq.gz	0:150 1:150	A:1245049988;C:1109235648;G:1268915785;T:1209053869;N:74210	150	150	1245049988	1109235648	1268915785	1209053869	74210	SRX21590031	SRS18767605	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63782	0.64502	0.08987	0.09231	0.72234	0.72196	0.49523	0.49588	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25837	25837	SRR25868753	SRX21590030	SRS18767604	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.				Pa5	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56779\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep5\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa5 S1	Pa5 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		Pa5_S1_L001_R1_001.fastq.gz Pa5_S1_L001_R2_001.fastq.gz	fastq fastq	11549379600.0	38497932.0	Pa5 S1 L001 R1 001.fastq.gz	0:150 1:150	A:3027043529;C:2622862227;G:2939280467;T:2959957175;N:236202	150	150	3027043529	2622862227	2939280467	2959957175	236202	SRX21590030	SRS18767604	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67886	0.68486	0.10231	0.10649	0.71601	0.7163	0.48106	0.49898	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25838	25838	SRR25868754	SRX21590029	SRS18767602	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.				Pa3	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56778\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep4\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa3 S1	Pa3 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		Pa3_S1_L001_R1_001.fastq.gz Pa3_S1_L001_R2_001.fastq.gz	fastq fastq	7038052800.0	23460176.0	Pa3 S1 L001 R1 001.fastq.gz	0:150 1:150	A:1845229826;C:1597202687;G:1831639368;T:1763932214;N:48705	150	150	1845229826	1597202687	1831639368	1763932214	48705	SRX21590029	SRS18767602	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66478	0.67117	0.08459	0.08634	0.71151	0.71001	0.4755	0.48472	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25839	25839	SRR25868755	SRX21590028	SRS18767601	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.				Pa1	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56777\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep3\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa1 S128	Pa1 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		Pa1_S128_L002_R1_001.fastq.gz Pa1_S128_L002_R2_001.fastq.gz	fastq fastq	9182487600.0	30608292.0	Pa1 S128 L002 R1 001.fastq.gz	0:150 1:150	A:2380195651;C:2107770795;G:2380907607;T:2313544754;N:68793	150	150	2380195651	2107770795	2380907607	2313544754	68793	SRX21590028	SRS18767601	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67336	0.68312	0.10238	0.10612	0.71218	0.71153	0.5069	0.50884	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25840	25840	SRR25868756	SRX21590027	SRS18767599	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.				Pa14	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56776\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa14 S379	Pa14 S379	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		Pa14_S379_L004_R1_001.fastq.gz Pa14_S379_L004_R2_001.fastq.gz	fastq fastq	7008344400.0	23361148.0	Pa14 S379 L004 R1 001.fastq.gz	0:150 1:150	A:1835137668;C:1572616966;G:1805917991;T:1794612968;N:58807	150	150	1835137668	1572616966	1805917991	1794612968	58807	SRX21590027	SRS18767599	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.6576	0.66306	0.09119	0.09429	0.71052	0.71153	0.47292	0.48471	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25841	25841	SRR25868757	SRX21590026	SRS18767600	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.				Pa10	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56775\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep1\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pa10 S189	Pa10 S189	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		Pa10_S189_L002_R1_001.fastq.gz Pa10_S189_L002_R2_001.fastq.gz	fastq fastq	5521604400.0	18405348.0	Pa10 S189 L002 R1 001.fastq.gz	0:150 1:150	A:1445351288;C:1243777974;G:1444075256;T:1388284775;N:115107	150	150	1445351288	1243777974	1444075256	1388284775	115107	SRX21590026	SRS18767600	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.63972	0.648	0.08594	0.08862	0.71534	0.71344	0.48743	0.49141	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
25908	25908	SRR25868480	SRX21589959	SRS18767530	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.				T2Aa6	strain:AB wild type\|age:6 hpf 48 hpf\|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 56261\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:2\|dose: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	T2Aa6 S148	T2Aa6 S148	At the end of each PFAS exposure period zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP457982		T2Aa6_S148_L002_R1_001.fastq.gz T2Aa6_S148_L002_R2_001.fastq.gz	fastq fastq	7134441000.0	23781470.0	T2Aa6 S148 L002 R1 001.fastq.gz	0:150 1:150	A:1806347597;C:1652831414;G:1932965373;T:1742243623;N:52993	150	150	1806347597	1652831414	1932965373	1742243623	52993	SRX21589959	SRS18767530	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.60052	0.60248	0.08187	0.08305	0.75128	0.75041	0.48822	0.49497	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26016	26016	SRR25868588	SRX21589851	SRS18767424	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.				T5VAa5	strain:AB wild type\|age:24 hpf 120 hpf\|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 55876\|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:5\|dose:0\|dose units:ug/L\|treatment:VehicleControl\|replicate ID:rep2\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo control	T5VAa5 S217	T5VAa5 S217	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		T5VAa5_S217_L002_R1_001.fastq.gz T5VAa5_S217_L002_R2_001.fastq.gz	fastq fastq	8100529500.0	27001765.0	T5VAa5 S217 L002 R1 001.fastq.gz	0:150 1:150	A:2094646242;C:1839873833;G:2144213073;T:2021734883;N:61469	150	150	2094646242	1839873833	2144213073	2021734883	61469	SRX21589851	SRS18767424	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61505	0.62102	0.08204	0.08402	0.72581	0.72545	0.499	0.50086	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Multi-stage	Trunk	Surface Structure
26080	26080	SRR25868308	SRX21589787	SRS18767360	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.				T2Af6	strain:AB wild type\|age:6 hpf 48 hpf\|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 56286\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:2\|dose:159.79631931590794\|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	T2Af6 S279	T2Af6 S279	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		T2Af6_S279_L003_R1_001.fastq.gz T2Af6_S279_L003_R2_001.fastq.gz	fastq fastq	5528429100.0	18428097.0	T2Af6 S279 L003 R1 001.fastq.gz	0:150 1:150	A:1433841596;C:1256938964;G:1439924335;T:1397674606;N:49599	150	150	1433841596	1256938964	1439924335	1397674606	49599	SRX21589787	SRS18767360	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.61375	0.62041	0.09152	0.09319	0.7516	0.75134	0.48727	0.49337	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26082	26082	SRR25868310	SRX21589785	SRS18767357	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.				T2Af3	strain:AB wild type\|age:6 hpf 48 hpf\|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 56284\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:2\|dose:159.79631931590794\|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	T2Af3 S153	T2Af3 S153	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		T2Af3_S153_L002_R1_001.fastq.gz T2Af3_S153_L002_R2_001.fastq.gz	fastq fastq	5379874200.0	17932914.0	T2Af3 S153 L002 R1 001.fastq.gz	0:150 1:150	A:1402934987;C:1214102472;G:1426676017;T:1336121878;N:38846	150	150	1402934987	1214102472	1426676017	1336121878	38846	SRX21589785	SRS18767357	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.64104	0.6473	0.09457	0.09657	0.74696	0.74489	0.4865	0.49282	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26267	26267	SRR25868151	SRX21589600	SRS18767173	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.				Pb8	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56788\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep14\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb8 S2	Pb8 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		Pb8_S2_L001_R1_001.fastq.gz Pb8_S2_L001_R2_001.fastq.gz	fastq fastq	6086321700.0	20287739.0	Pb8 S2 L001 R1 001.fastq.gz	0:150 1:150	A:1592326945;C:1394299116;G:1564764929;T:1534890714;N:39996	150	150	1592326945	1394299116	1564764929	1534890714	39996	SRX21589600	SRS18767173	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.65709	0.65986	0.08857	0.0902	0.71482	0.71638	0.48561	0.48653	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26268	26268	SRR25868152	SRX21589599	SRS18767172	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.				Pb7	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56787\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep13\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb7 S61	Pb7 S61	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		Pb7_S61_L001_R1_001.fastq.gz Pb7_S61_L001_R2_001.fastq.gz	fastq fastq	4593925500.0	15313085.0	Pb7 S61 L001 R1 001.fastq.gz	0:150 1:150	A:1190256800;C:1057716685;G:1190108722;T:1155745556;N:97737	150	150	1190256800	1057716685	1190108722	1155745556	97737	SRX21589599	SRS18767172	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.66629	0.67669	0.09941	0.10242	0.71745	0.71634	0.49826	0.49652	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26269	26269	SRR25868153	SRX21589598	SRS18767171	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.				Pb4	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56786\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep12\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb4 S380	Pb4 S380	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		Pb4_S380_L004_R1_001.fastq.gz Pb4_S380_L004_R2_001.fastq.gz	fastq fastq	8164445100.0	27214817.0	Pb4 S380 L004 R1 001.fastq.gz	0:150 1:150	A:2155703367;C:1850880757;G:2027564430;T:2130226550;N:69996	150	150	2155703367	1850880757	2027564430	2130226550	69996	SRX21589598	SRS18767171	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.7134	0.72474	0.11491	0.12017	0.70737	0.70692	0.49565	0.50548	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26270	26270	SRR25868154	SRX21589597	SRS18767170	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.				Pb2	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56785\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep11\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb2 S255	Pb2 S255	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		Pb2_S255_L003_R1_001.fastq.gz Pb2_S255_L003_R2_001.fastq.gz	fastq fastq	7995102000.0	26650340.0	Pb2 S255 L003 R1 001.fastq.gz	0:150 1:150	A:2079002717;C:1812957930;G:2062775860;T:2040295802;N:69691	150	150	2079002717	1812957930	2062775860	2040295802	69691	SRX21589597	SRS18767170	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.67008	0.67762	0.09897	0.10299	0.71443	0.71451	0.4974	0.49463	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
26271	26271	SRR25868155	SRX21589596	SRS18767169	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.				Pb13	strain:AB wild type\|age:not applicable\|dev stage:embryo\|collection date:2022\|geo loc name:USA: Minnesota Duluth\|sex:not applicable\|tissue:whole body zebrafish embryo\|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division 6201 Congdon Blvd Duluth MN 56784\|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth MN. The fish were raised in a flow through system with control UV treated filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 ± 1°C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning approximately 2 hours post the lights turned on embryos were collected and maintained in filtered LSW in an incubator set at 28.5°C. At approximately 4 hpf zebrafish embryos were screened under a stereo microscope and only similarly staged embryos were sorted out for chemical exposure. All dead malformed and unfertilized eggs were discarded.\|collected by:Great Lakes Toxicology & Ecology Division\|sample type:Total RNA\|time code:NA\|dose:NA\|dose units:ug/L\|treatment:std RNA pool\|replicate ID:rep10\|repeat sample:No\|BioSampleModel:Model organism or animal									RNA Seq of danio rerio: whole organism embryo unexposed QA	Pb13 S253	Pb13 S253	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		Pb13_S253_L002_R1_001.fastq.gz Pb13_S253_L002_R2_001.fastq.gz	fastq fastq	5289369900.0	17631233.0	Pb13 S253 L002 R1 001.fastq.gz	0:150 1:150	A:1397410193;C:1180528245;G:1345935530;T:1365385200;N:110732	150	150	1397410193	1180528245	1345935530	1365385200	110732	SRX21589596	SRS18767169	SRA1703738	U.S. Environmental Protection Agency\|Great Lakes Toxicology and Ecology Division	U.S. Environmental Protection Agency	2	0.62751	0.63838	0.07975	0.08251	0.71088	0.7111	0.47999	0.47758	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	lexogen	bulk	unknown	unknown	United States	2023-09-01	Multi-stage	Embryo	Trunk	Surface Structure
33164	33164	SRR29809736	SRX25309007	SRS21984115	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 5	GSM8393514	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393514	GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq	GSM8393514 r1	GSM8393514	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		6_2.fq.gz 6_1.fq.gz	fastq fastq	4827420200.0	24137101.0	GSM8393514 r1	0:100 1:100	A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0	100	100	1278807278	1130198430	1150325506	1268088986	0	SRX25309007	SRS21984115	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9409	0.94542	0.08059	0.07981	0.69021	0.68887	0.47275	0.47095	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33165	33165	SRR29809737	SRX25309006	SRS21984114	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 4	GSM8393513	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393513	GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq	GSM8393513 r1	GSM8393513	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		30_2.fq.gz 30_1.fq.gz	fastq fastq	4240862400.0	21204312.0	GSM8393513 r1	0:100 1:100	A:1146088921;C:972830110;G:990127288;T:1131816081;N:0	100	100	1146088921	972830110	990127288	1131816081	0	SRX25309006	SRS21984114	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.93888	0.9444	0.08826	0.08671	0.70431	0.70212	0.48083	0.48199	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33166	33166	SRR29809738	SRX25309005	SRS21984113	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 3	GSM8393512	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393512	GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq	GSM8393512 r1	GSM8393512	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		24_2.fq.gz 24_1.fq.gz	fastq fastq	4822516400.0	24112582.0	GSM8393512 r1	0:100 1:100	A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0	100	100	1276866727	1130641795	1148897951	1266109927	0	SRX25309005	SRS21984113	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94126	0.94446	0.07837	0.07762	0.6911	0.69037	0.46251	0.4642	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33167	33167	SRR29809739	SRX25309004	SRS21984112	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 2	GSM8393511	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393511	GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq	GSM8393511 r1	GSM8393511	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		18_2.fq.gz 18_1.fq.gz	fastq fastq	4820332000.0	24101660.0	GSM8393511 r1	0:100 1:100	A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0	100	100	1306037553	1103383630	1122255994	1288654823	0	SRX25309004	SRS21984112	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94035	0.9445	0.08468	0.08417	0.71106	0.70897	0.47897	0.47969	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33168	33168	SRR29809740	SRX25309003	SRS21984111	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 20mM STS 1	GSM8393510	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 20mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:20\|agent:STS	GSM8393510	GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq	GSM8393510 r1	GSM8393510	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		12_1.fq.gz 12_2.fq.gz	fastq fastq	4825742600.0	24128713.0	GSM8393510 r1	0:100 1:100	A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0	100	100	1264457552	1145133600	1160084092	1256067356	0	SRX25309003	SRS21984111	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94613	0.9501	0.06915	0.06812	0.68941	0.68852	0.45659	0.45507	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33169	33169	SRR29809741	SRX25309002	SRS21984110	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 5	GSM8393509	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393509	GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq	GSM8393509 r1	GSM8393509	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		5_2.fq.gz 5_1.fq.gz	fastq fastq	4816068800.0	24080344.0	GSM8393509 r1	0:100 1:100	A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0	100	100	1278638535	1126555210	1141985166	1268889889	0	SRX25309002	SRS21984110	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9414	0.94516	0.08012	0.07915	0.69284	0.69185	0.46526	0.46882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33170	33170	SRR29809742	SRX25309001	SRS21984109	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 4	GSM8393508	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393508	GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq	GSM8393508 r1	GSM8393508	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		29_2.fq.gz 29_1.fq.gz	fastq fastq	4386218400.0	21931092.0	GSM8393508 r1	0:100 1:100	A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0	100	100	1181773341	1011246416	1025789654	1167408989	0	SRX25309001	SRS21984109	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94168	0.94587	0.08215	0.08003	0.69682	0.69544	0.47251	0.47607	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33171	33171	SRR29809743	SRX25309000	SRS21984108	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 3	GSM8393507	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393507	GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq	GSM8393507 r1	GSM8393507	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		23_2.fq.gz 23_1.fq.gz	fastq fastq	4808808800.0	24044044.0	GSM8393507 r1	0:100 1:100	A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0	100	100	1269564907	1132101674	1149286214	1257856005	0	SRX25309000	SRS21984108	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9434	0.94774	0.07109	0.0703	0.69264	0.69183	0.45908	0.46455	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33172	33172	SRR29809744	SRX25308999	SRS21984107	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 2	GSM8393506	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393506	GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq	GSM8393506 r1	GSM8393506	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		17_1.fq.gz 17_2.fq.gz	fastq fastq	4805883400.0	24029417.0	GSM8393506 r1	0:100 1:100	A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0	100	100	1299291748	1102517917	1122450422	1281623313	0	SRX25308999	SRS21984107	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94253	0.9461	0.08371	0.08155	0.70589	0.70423	0.4853	0.47925	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33173	33173	SRR29809745	SRX25308998	SRS21984106	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 15mM STS 1	GSM8393505	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 15mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:15\|agent:STS	GSM8393505	GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq	GSM8393505 r1	GSM8393505	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		11_1.fq.gz 11_2.fq.gz	fastq fastq	4812111600.0	24060558.0	GSM8393505 r1	0:100 1:100	A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0	100	100	1269803704	1133657948	1150461915	1258188033	0	SRX25308998	SRS21984106	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94311	0.94708	0.07444	0.07235	0.69266	0.69158	0.46689	0.46584	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33174	33174	SRR29809746	SRX25308997	SRS21984105	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 5	GSM8393504	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393504	GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq	GSM8393504 r1	GSM8393504	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		4_2.fq.gz 4_1.fq.gz	fastq fastq	4804978800.0	24024894.0	GSM8393504 r1	0:100 1:100	A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0	100	100	1266882676	1131396187	1149418875	1257281062	0	SRX25308997	SRS21984105	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94345	0.94707	0.07428	0.0741	0.6898	0.68856	0.4653	0.46918	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33175	33175	SRR29809747	SRX25308996	SRS21984104	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 4	GSM8393503	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393503	GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq	GSM8393503 r1	GSM8393503	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		28_1.fq.gz 28_2.fq.gz	fastq fastq	4464066400.0	22320332.0	GSM8393503 r1	0:100 1:100	A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0	100	100	1209155509	1023407835	1040239673	1191263383	0	SRX25308996	SRS21984104	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.934	0.93723	0.08814	0.08601	0.69834	0.69798	0.47533	0.47611	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33176	33176	SRR29809748	SRX25308995	SRS21984103	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 3	GSM8393502	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393502	GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq	GSM8393502 r1	GSM8393502	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		22_1.fq.gz 22_2.fq.gz	fastq fastq	4613819800.0	23069099.0	GSM8393502 r1	0:100 1:100	A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0	100	100	1218890904	1084874278	1104087523	1205967095	0	SRX25308995	SRS21984103	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9426	0.94852	0.07601	0.07487	0.69197	0.69075	0.45872	0.45856	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33177	33177	SRR29809749	SRX25308994	SRS21984102	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 2	GSM8393501	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393501	GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq	GSM8393501 r1	GSM8393501	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		16_1.fq.gz 16_2.fq.gz	fastq fastq	4818005000.0	24090025.0	GSM8393501 r1	0:100 1:100	A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0	100	100	1291680744	1114433015	1134463270	1277427971	0	SRX25308994	SRS21984102	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.93988	0.94257	0.08614	0.08554	0.69376	0.69367	0.47178	0.47111	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33178	33178	SRR29809750	SRX25308993	SRS21984101	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		pdx1 morpholino + 0mM STS 1	GSM8393500	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	pdx1 morpholino + 0mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:pdx1\|dose:0\|agent:STS	GSM8393500	GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq	GSM8393500 r1	GSM8393500	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		10_2.fq.gz 10_1.fq.gz	fastq fastq	4827935800.0	24139679.0	GSM8393500 r1	0:100 1:100	A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0	100	100	1267823750	1143323623	1156194469	1260593958	0	SRX25308993	SRS21984101	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94483	0.94829	0.07178	0.07025	0.69077	0.69025	0.46181	0.45982	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33179	33179	SRR29809751	SRX25308992	SRS21984100	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 5	GSM8393499	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393499	GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq	GSM8393499 r1	GSM8393499	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		9_1.fq.gz 9_2.fq.gz	fastq fastq	4822379000.0	24111895.0	GSM8393499 r1	0:100 1:100	A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0	100	100	1262977318	1145277730	1159167028	1254956924	0	SRX25308992	SRS21984100	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94642	0.94964	0.06863	0.0674	0.69288	0.69252	0.4574	0.44372	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33180	33180	SRR29809752	SRX25308991	SRS21984099	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 4	GSM8393498	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393498	GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq	GSM8393498 r1	GSM8393498	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		3_1.fq.gz 3_2.fq.gz	fastq fastq	4803150200.0	24015751.0	GSM8393498 r1	0:100 1:100	A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0	100	100	1253239300	1144350399	1158671984	1246888517	0	SRX25308991	SRS21984099	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94606	0.95015	0.06543	0.06441	0.68676	0.68611	0.44857	0.44396	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33181	33181	SRR29809753	SRX25308990	SRS21984098	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 3	GSM8393497	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393497	GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq	GSM8393497 r1	GSM8393497	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		27_1.fq.gz 27_2.fq.gz	fastq fastq	4277827200.0	21389136.0	GSM8393497 r1	0:100 1:100	A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0	100	100	1142589086	997230367	1005771965	1132235782	0	SRX25308990	SRS21984098	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94201	0.94596	0.07754	0.07484	0.69794	0.69617	0.46286	0.45985	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33182	33182	SRR29809754	SRX25308989	SRS21984097	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 2	GSM8393496	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393496	GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq	GSM8393496 r1	GSM8393496	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		21_2.fq.gz 21_1.fq.gz	fastq fastq	4019456600.0	20097283.0	GSM8393496 r1	0:100 1:100	A:1053249649;C:953992221;G:968100759;T:1044113971;N:0	100	100	1053249649	953992221	968100759	1044113971	0	SRX25308989	SRS21984097	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94377	0.95125	0.06861	0.06745	0.68676	0.68523	0.45049	0.45168	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33183	33183	SRR29809755	SRX25308988	SRS21984096	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 20mM STS 1	GSM8393495	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 20mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:20\|agent:STS	GSM8393495	GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq	GSM8393495 r1	GSM8393495	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		15_1.fq.gz 15_2.fq.gz	fastq fastq	4829679200.0	24148396.0	GSM8393495 r1	0:100 1:100	A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0	100	100	1292193191	1119414896	1140502241	1277568872	0	SRX25308988	SRS21984096	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9423	0.9467	0.07958	0.07808	0.69763	0.69658	0.46406	0.46623	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33184	33184	SRR29809756	SRX25308987	SRS21984095	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 5	GSM8393494	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393494	GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq	GSM8393494 r1	GSM8393494	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		8_2.fq.gz 8_1.fq.gz	fastq fastq	4803709800.0	24018549.0	GSM8393494 r1	0:100 1:100	A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0	100	100	1253733589	1143748058	1158768340	1247459813	0	SRX25308987	SRS21984095	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94718	0.94926	0.06582	0.06461	0.68791	0.68738	0.44759	0.44517	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33185	33185	SRR29809757	SRX25308986	SRS21984094	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 4	GSM8393493	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393493	GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq	GSM8393493 r1	GSM8393493	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		26_1.fq.gz 26_2.fq.gz	fastq fastq	4816718000.0	24083590.0	GSM8393493 r1	0:100 1:100	A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0	100	100	1278966223	1129131703	1144234415	1264385659	0	SRX25308986	SRS21984094	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94278	0.94713	0.07235	0.0704	0.69895	0.698	0.4536	0.45416	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33186	33186	SRR29809758	SRX25308985	SRS21984093	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 3	GSM8393492	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393492	GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq	GSM8393492 r1	GSM8393492	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		20_2.fq.gz 20_1.fq.gz	fastq fastq	4825880400.0	24129402.0	GSM8393492 r1	0:100 1:100	A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0	100	100	1263053657	1147908238	1161094243	1253824262	0	SRX25308985	SRS21984093	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94642	0.95164	0.06472	0.06312	0.69035	0.68909	0.44854	0.44216	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33187	33187	SRR29809759	SRX25308984	SRS21984092	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 2	GSM8393491	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393491	GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq	GSM8393491 r1	GSM8393491	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		2_1.fq.gz 2_2.fq.gz	fastq fastq	4805985200.0	24029926.0	GSM8393491 r1	0:100 1:100	A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0	100	100	1255841114	1143278337	1157783615	1249082134	0	SRX25308984	SRS21984092	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94666	0.94794	0.06553	0.06456	0.69181	0.69175	0.4359	0.44559	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33188	33188	SRR29809760	SRX25308983	SRS21984091	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 15mM STS 1	GSM8393490	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 15mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:15\|agent:STS	GSM8393490	GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq	GSM8393490 r1	GSM8393490	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		14_1.fq.gz 14_2.fq.gz	fastq fastq	4553465000.0	22767325.0	GSM8393490 r1	0:100 1:100	A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0	100	100	1209891078	1063666819	1082075995	1197831108	0	SRX25308983	SRS21984091	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.9432	0.94661	0.07696	0.07599	0.69763	0.69721	0.46463	0.46425	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33189	33189	SRR29809761	SRX25308982	SRS21984090	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 5	GSM8393489	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393489	GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq	GSM8393489 r1	GSM8393489	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		7_1.fq.gz 7_2.fq.gz	fastq fastq	4813770200.0	24068851.0	GSM8393489 r1	0:100 1:100	A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0	100	100	1251918123	1151936172	1164458418	1245457487	0	SRX25308982	SRS21984090	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.95021	0.95271	0.06538	0.06376	0.69171	0.68996	0.44317	0.4435	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33190	33190	SRR29809762	SRX25308981	SRS21984089	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 4	GSM8393488	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393488	GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq	GSM8393488 r1	GSM8393488	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		25_1.fq.gz 25_2.fq.gz	fastq fastq	4810346800.0	24051734.0	GSM8393488 r1	0:100 1:100	A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0	100	100	1275301780	1127999390	1144547869	1262497761	0	SRX25308981	SRS21984089	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94519	0.94834	0.06949	0.06803	0.69552	0.69524	0.44741	0.45052	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33191	33191	SRR29809763	SRX25308980	SRS21984088	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 3	GSM8393487	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393487	GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq	GSM8393487 r1	GSM8393487	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		19_1.fq.gz 19_2.fq.gz	fastq fastq	4811704200.0	24058521.0	GSM8393487 r1	0:100 1:100	A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0	100	100	1257129134	1146835083	1160663520	1247076463	0	SRX25308980	SRS21984088	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94691	0.95082	0.06344	0.06212	0.69014	0.69059	0.45386	0.43864	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33192	33192	SRR29809764	SRX25308979	SRS21984087	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 2	GSM8393486	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393486	GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq	GSM8393486 r1	GSM8393486	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		13_1.fq.gz 13_2.fq.gz	fastq fastq	4616178800.0	23080894.0	GSM8393486 r1	0:100 1:100	A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0	100	100	1225429879	1079094541	1096304865	1215349515	0	SRX25308979	SRS21984087	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94498	0.9498	0.07635	0.075	0.69319	0.6927	0.46598	0.466	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
33193	33193	SRR29809765	SRX25308978	SRS21984086	SRP519612	PRJNA1135151	The effect of sodium thiosulfate on hyperglycemic zebrafish larvae	GSE272119	Transcriptome Analysis	We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene both metabolomically and transcriptionally. Notably treatment with STS led to a compensatory upregulation of NO signaling as evidenced by preliminary metabolomic data ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS RNA seq of hyperglycemic zebrafish treated with 0 mM 15 mM and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1 which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis a metabolomic profiling of similar experimental groups was performed.	pubmed:39264236		Control morpholino + 0mM STS 1	GSM8393485	source name:larvae\|tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS\|geo loc name:missing\|collection date:missing	Control morpholino + 0mM STS 1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates generated with cpm function from edgeR version 3.17	larvae		RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		tissue:larvae\|strain:Tgwt1b:EGFP\|genotype:ctrl\|dose:0\|agent:STS	GSM8393485	GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq	GSM8393485 r1	GSM8393485	1	RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden 173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP519612		1_1.fq.gz 1_2.fq.gz	fastq fastq	4823953400.0	24119767.0	GSM8393485 r1	0:100 1:100	A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0	100	100	1270954678	1137736456	1155516940	1259745326	0	SRX25308978	SRS21984086	SRA1923353	ZMF, University Heidelberg	ZMF, University Heidelberg	2	0.94325	0.94699	0.06928	0.06864	0.69372	0.69307	0.44844	0.45647	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2024-07-12	Multi-stage	Multi-stage	Trunk	Surface Structure
34206	34206	SRR31539731	SRX26906755	SRS23386341	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf sox10 mutant embryos biol rep 3	GSM8655460	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf sox10 mutant embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:7 dpf	GSM8655460	GSM8655460: Whole body 7 dpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq	GSM8655460 r1	GSM8655460	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_mut 3_R1.fastq.gz 7 dpf_mut 3_R2.fastq.gz	fastq fastq	14265929756.0	47238178.0	GSM8655460 r1	0:151 1:151	A:3890017873;C:3282588566;G:3079614796;T:4012518928;N:1189593	151	151	3890017873	3282588566	3079614796	4012518928	1189593	SRX26906755	SRS23386341			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34207	34207	SRR31539732	SRX26906754	SRS23386340	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf sox10 mutant embryos biol rep 2	GSM8655459	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf sox10 mutant embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:7 dpf	GSM8655459	GSM8655459: Whole body 7 dpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq	GSM8655459 r1	GSM8655459	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_mut 2_R1.fastq.gz 7 dpf_mut 2_R2.fastq.gz	fastq fastq	16096968138.0	53301219.0	GSM8655459 r1	0:151 1:151	A:4158085994;C:3672102993;G:3915623401;T:4349806816;N:1348934	151	151	4158085994	3672102993	3915623401	4349806816	1348934	SRX26906754	SRS23386340			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34208	34208	SRR31539733	SRX26906753	SRS23386339	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf sox10 mutant embryos biol rep 1	GSM8655458	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf sox10 mutant embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:7 dpf	GSM8655458	GSM8655458: Whole body 7 dpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq	GSM8655458 r1	GSM8655458	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_mut 1_R1.fastq.gz 7 dpf_mut 1_R2.fastq.gz	fastq fastq	15919165034.0	52712467.0	GSM8655458 r1	0:151 1:151	A:4153549187;C:3626188288;G:3782139805;T:4355972996;N:1314758	151	151	4153549187	3626188288	3782139805	4355972996	1314758	SRX26906753	SRS23386339			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34209	34209	SRR31539734	SRX26906752	SRS23386338	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf wild type embryos biol rep 3	GSM8655457	source name:whole body\|tissue:whole body\|genotype:WT\|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf wild type embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:7 dpf	GSM8655457	GSM8655457: Whole body 7 dpf wild type embryos biol rep 3; Danio rerio; RNA Seq	GSM8655457 r1	GSM8655457	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_WT 3_R1.fastq.gz 7 dpf_WT 3_R2.fastq.gz	fastq fastq	15543953590.0	51470045.0	GSM8655457 r1	0:151 1:151	A:4031818994;C:3704599213;G:3577251498;T:4228986622;N:1297263	151	151	4031818994	3704599213	3577251498	4228986622	1297263	SRX26906752	SRS23386338			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34210	34210	SRR31539735	SRX26906751	SRS23386337	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf wild type embryos biol rep 2	GSM8655456	source name:whole body\|tissue:whole body\|genotype:WT\|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf wild type embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:7 dpf	GSM8655456	GSM8655456: Whole body 7 dpf wild type embryos biol rep 2; Danio rerio; RNA Seq	GSM8655456 r1	GSM8655456	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_WT 2_R1.fastq.gz 7 dpf_WT 2_R2.fastq.gz	fastq fastq	14325089744.0	47434072.0	GSM8655456 r1	0:151 1:151	A:3806636861;C:3343198938;G:3185927363;T:3988104951;N:1221631	151	151	3806636861	3343198938	3185927363	3988104951	1221631	SRX26906751	SRS23386337			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34211	34211	SRR31539736	SRX26906750	SRS23386333	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 7 dpf wild type embryos biol rep 1	GSM8655455	source name:whole body\|tissue:whole body\|genotype:WT\|time:7 dpf\|geo loc name:missing\|collection date:missing	Whole body 7 dpf wild type embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:7 dpf	GSM8655455	GSM8655455: Whole body 7 dpf wild type embryos biol rep 1; Danio rerio; RNA Seq	GSM8655455 r1	GSM8655455	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		7 dpf_WT 1_R1.fastq.gz 7 dpf_WT 1_R2.fastq.gz	fastq fastq	16398118008.0	54298404.0	GSM8655455 r1	0:151 1:151	A:4341778579;C:3858758690;G:3657590940;T:4538608543;N:1381256	151	151	4341778579	3858758690	3657590940	4538608543	1381256	SRX26906750	SRS23386333			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34212	34212	SRR31539737	SRX26906749	SRS23386334	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf sox10 mutant embryos biol rep 3	GSM8655454	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf sox10 mutant embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:4 dpf	GSM8655454	GSM8655454: Whole body 4 dpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq	GSM8655454 r1	GSM8655454	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_mut 3_R1.fastq.gz 4 dpf_mut 3_R2.fastq.gz	fastq fastq	15071278894.0	49904897.0	GSM8655454 r1	0:151 1:151	A:3996223512;C:3537174277;G:3398338576;T:4138304072;N:1238457	151	151	3996223512	3537174277	3398338576	4138304072	1238457	SRX26906749	SRS23386334			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34213	34213	SRR31539738	SRX26906748	SRS23386336	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf sox10 mutant embryos biol rep 2	GSM8655453	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf sox10 mutant embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:4 dpf	GSM8655453	GSM8655453: Whole body 4 dpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq	GSM8655453 r1	GSM8655453	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_mut 2_R1.fastq.gz 4 dpf_mut 2_R2.fastq.gz	fastq fastq	14918687958.0	49399629.0	GSM8655453 r1	0:151 1:151	A:3994132161;C:3464356999;G:3293001897;T:4165943265;N:1253636	151	151	3994132161	3464356999	3293001897	4165943265	1253636	SRX26906748	SRS23386336			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34214	34214	SRR31539739	SRX26906747	SRS23386332	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf sox10 mutant embryos biol rep 1	GSM8655452	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf sox10 mutant embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:4 dpf	GSM8655452	GSM8655452: Whole body 4 dpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq	GSM8655452 r1	GSM8655452	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_mut 1_R1.fastq.gz 4 dpf_mut 1_R2.fastq.gz	fastq fastq	14573247372.0	48255786.0	GSM8655452 r1	0:151 1:151	A:3964700989;C:3340575136;G:3128233836;T:4138502375;N:1235036	151	151	3964700989	3340575136	3128233836	4138502375	1235036	SRX26906747	SRS23386332			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34215	34215	SRR31539740	SRX26906746	SRS23386331	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf wild type embryos biol rep 3	GSM8655451	source name:whole body\|tissue:whole body\|genotype:WT\|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf wild type embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:4 dpf	GSM8655451	GSM8655451: Whole body 4 dpf wild type embryos biol rep 3; Danio rerio; RNA Seq	GSM8655451 r1	GSM8655451	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_WT 3_R1.fastq.gz 4 dpf_WT 3_R2.fastq.gz	fastq fastq	15132219172.0	50106686.0	GSM8655451 r1	0:151 1:151	A:4030654907;C:3519071260;G:3404455031;T:4176756699;N:1281275	151	151	4030654907	3519071260	3404455031	4176756699	1281275	SRX26906746	SRS23386331			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34216	34216	SRR31539741	SRX26906745	SRS23386335	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf wild type embryos biol rep 2	GSM8655450	source name:whole body\|tissue:whole body\|genotype:WT\|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf wild type embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:4 dpf	GSM8655450	GSM8655450: Whole body 4 dpf wild type embryos biol rep 2; Danio rerio; RNA Seq	GSM8655450 r1	GSM8655450	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_WT 2_R1.fastq.gz 4 dpf_WT 2_R2.fastq.gz	fastq fastq	15546478914.0	51478407.0	GSM8655450 r1	0:151 1:151	A:4105803894;C:3606318412;G:3589944905;T:4243130619;N:1281084	151	151	4105803894	3606318412	3589944905	4243130619	1281084	SRX26906745	SRS23386335			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34217	34217	SRR31539742	SRX26906744	SRS23386330	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 4 dpf wild type embryos biol rep 1	GSM8655449	source name:whole body\|tissue:whole body\|genotype:WT\|time:4 dpf\|geo loc name:missing\|collection date:missing	Whole body 4 dpf wild type embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:4 dpf	GSM8655449	GSM8655449: Whole body 4 dpf wild type embryos biol rep 1; Danio rerio; RNA Seq	GSM8655449 r1	GSM8655449	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		4 dpf_WT 1_R1.fastq.gz 4 dpf_WT 1_R2.fastq.gz	fastq fastq	15246602880.0	50485440.0	GSM8655449 r1	0:151 1:151	A:4017771448;C:3536729749;G:3495956173;T:4194910365;N:1235145	151	151	4017771448	3536729749	3495956173	4194910365	1235145	SRX26906744	SRS23386330			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34218	34218	SRR31539743	SRX26906743	SRS23386329	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf sox10 mutant embryos biol rep 3	GSM8655448	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf sox10 mutant embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:45 hpf	GSM8655448	GSM8655448: Whole body 45 hpf sox10 mutant embryos biol rep 3; Danio rerio; RNA Seq	GSM8655448 r1	GSM8655448	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_mut 3_R1.fastq.gz 45 hpf_mut 3_R2.fastq.gz	fastq fastq	14338321572.0	47477886.0	GSM8655448 r1	0:151 1:151	A:3808719246;C:3382555065;G:3212075099;T:3933758367;N:1213795	151	151	3808719246	3382555065	3212075099	3933758367	1213795	SRX26906743	SRS23386329			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34219	34219	SRR31539744	SRX26906742	SRS23386326	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf sox10 mutant embryos biol rep 2	GSM8655447	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf sox10 mutant embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:45 hpf	GSM8655447	GSM8655447: Whole body 45 hpf sox10 mutant embryos biol rep 2; Danio rerio; RNA Seq	GSM8655447 r1	GSM8655447	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_mut 2_R1.fastq.gz 45 hpf_mut 2_R2.fastq.gz	fastq fastq	15462167158.0	51199229.0	GSM8655447 r1	0:151 1:151	A:4089691508;C:3622289242;G:3495097207;T:4253826187;N:1263014	151	151	4089691508	3622289242	3495097207	4253826187	1263014	SRX26906742	SRS23386326			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34220	34220	SRR31539745	SRX26906741	SRS23386327	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf sox10 mutant embryos biol rep 1	GSM8655446	source name:whole body\|tissue:whole body\|genotype:sox10 / \|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf sox10 mutant embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:sox10 / \|time:45 hpf	GSM8655446	GSM8655446: Whole body 45 hpf sox10 mutant embryos biol rep 1; Danio rerio; RNA Seq	GSM8655446 r1	GSM8655446	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_mut 1_R1.fastq.gz 45 hpf_mut 1_R2.fastq.gz	fastq fastq	15655817712.0	51840456.0	GSM8655446 r1	0:151 1:151	A:4157360171;C:3674570903;G:3484564544;T:4338002005;N:1320089	151	151	4157360171	3674570903	3484564544	4338002005	1320089	SRX26906741	SRS23386327			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34221	34221	SRR31539746	SRX26906740	SRS23386328	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf wild type embryos biol rep 3	GSM8655445	source name:whole body\|tissue:whole body\|genotype:WT\|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf wild type embryos biol rep 3	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:45 hpf	GSM8655445	GSM8655445: Whole body 45 hpf wild type embryos biol rep 3; Danio rerio; RNA Seq	GSM8655445 r1	GSM8655445	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_WT 3_R1.fastq.gz 45 hpf_WT 3_R2.fastq.gz	fastq fastq	14580346184.0	48279292.0	GSM8655445 r1	0:151 1:151	A:3858927638;C:3450290173;G:3271701209;T:3998202503;N:1224661	151	151	3858927638	3450290173	3271701209	3998202503	1224661	SRX26906740	SRS23386328			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34222	34222	SRR31539747	SRX26906739	SRS23386325	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf wild type embryos biol rep 2	GSM8655444	source name:whole body\|tissue:whole body\|genotype:WT\|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf wild type embryos biol rep 2	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:45 hpf	GSM8655444	GSM8655444: Whole body 45 hpf wild type embryos biol rep 2; Danio rerio; RNA Seq	GSM8655444 r1	GSM8655444	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_WT 2_R1.fastq.gz 45 hpf_WT_2_R2.fastq.gz	fastq fastq	15005198878.0	49686089.0	GSM8655444 r1	0:151 1:151	A:3950487195;C:3509517845;G:3418800225;T:4125159820;N:1233793	151	151	3950487195	3509517845	3418800225	4125159820	1233793	SRX26906739	SRS23386325			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
34223	34223	SRR31539748	SRX26906738	SRS23386324	SRP548139	PRJNA1191617	Sox10 is required for systemic initiation of bone mineralization	GSE283071	Transcriptome Analysis	Heterozygous variants in SOX10 cause syndromes affecting pigmentation digestion hearing and neural development primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment resulting in severe calcium deficiency. As these ionocytes derive from ectoderm not crest we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a an anti hypercalcemic hormone in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf 4 dpf and 7 dpf. Total of 18 samples. 45 hpf 3 replicates: controls n = 10 20 & 25; mutants n = 10 15 & 15 embryos 4 dpf 3 replicates: controls n = 10 15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12 30 & 18; mutants = 18 12 & 7 embryos	pubmed:39791977		Whole body 45 hpf wild type embryos biol rep 1	GSM8655443	source name:whole body\|tissue:whole body\|genotype:WT\|time:45 hpf\|geo loc name:missing\|collection date:missing	Whole body 45 hpf wild type embryos biol rep 1	The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf 4 dpf and 7 dpf	whole body		RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit.		tissue:whole body\|genotype:WT\|time:45 hpf	GSM8655443	GSM8655443: Whole body 45 hpf wild type embryos biol rep 1; Danio rerio; RNA Seq	GSM8655443 r1	GSM8655443	1	RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq® stranded mRNA library preparation kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP548139		45 hpf_WT 1_R1.fastq.gz 45 hpf_WT 1_R2.fastq.gz	fastq fastq	14884992912.0	49288056.0	GSM8655443 r1	0:151 1:151	A:3878762924;C:3475070121;G:3485186845;T:4044768200;N:1204822	151	151	3878762924	3475070121	3485186845	4044768200	1204822	SRX26906738	SRS23386324			Barske Lab, Human Genetics, Cincinnati Children's Hospital												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	bulk	bulk	United States	2024-11-27	Multi-stage	Multi-stage	Trunk	Surface Structure
36227	36227	SRR33613672	SRX28842027	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD 3	HFD 3	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD-3-1.fq.gz HFD-3-2.fq.gz	fastq fastq	6810755100.0	22702517.0	HFD 3 1.fq.gz	0:150 1:150	A:1804127778;C:1596175018;G:1609090701;T:1801361603;N:0	150	150	1804127778	1596175018	1609090701	1801361603	0	SRX28842027	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36228	36228	SRR33613673	SRX28842026	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD 2	HFD 2	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD-2-1.fq.gz HFD-2-2.fq.gz	fastq fastq	6826358400.0	22754528.0	HFD 2 1.fq.gz	0:150 1:150	A:1826465185;C:1582322712;G:1596188986;T:1821381517;N:0	150	150	1826465185	1582322712	1596188986	1821381517	0	SRX28842026	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36229	36229	SRR33613674	SRX28842025	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD 1	HFD 1	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD-1-1.fq.gz HFD-1-2.fq.gz	fastq fastq	6598410300.0	21994701.0	HFD 1 1.fq.gz	0:150 1:150	A:1765905584;C:1529581410;G:1542056821;T:1760866485;N:0	150	150	1765905584	1529581410	1542056821	1760866485	0	SRX28842025	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36230	36230	SRR33613675	SRX28842024	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD10 3	HFD10 3	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD10-3-1.fq.gz HFD10-3-2.fq.gz	fastq fastq	6609153300.0	22030511.0	HFD10 3 1.fq.gz	0:150 1:150	A:1780787716;C:1521027085;G:1532800826;T:1774537673;N:0	150	150	1780787716	1521027085	1532800826	1774537673	0	SRX28842024	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36231	36231	SRR33613676	SRX28842023	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD10 2	HFD10 2	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD10-2-1.fq.gz HFD10-2-2.fq.gz	fastq fastq	6605145900.0	22017153.0	HFD10 2 1.fq.gz	0:150 1:150	A:1765731508;C:1533254667;G:1545960098;T:1760199627;N:0	150	150	1765731508	1533254667	1545960098	1760199627	0	SRX28842023	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36232	36232	SRR33613677	SRX28842022	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	HFD10 1	HFD10 1	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		HFD10-1-1.fq.gz HFD10-1-2.fq.gz	fastq fastq	6780056700.0	22600189.0	HFD10 1 1.fq.gz	0:150 1:150	A:1819443100;C:1566081115;G:1580525465;T:1814007020;N:0	150	150	1819443100	1566081115	1580525465	1814007020	0	SRX28842022	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36233	36233	SRR33613678	SRX28842021	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	NFD 3	NFD 3	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		NFD-3-1.fq.gz NFD-3-2.fq.gz	fastq fastq	6677775900.0	22259253.0	NFD 3 1.fq.gz	0:150 1:150	A:1794821611;C:1541478212;G:1552820105;T:1788655972;N:0	150	150	1794821611	1541478212	1552820105	1788655972	0	SRX28842021	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36234	36234	SRR33613679	SRX28842020	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	NFD 2	NFD 2	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		NFD-2-1.fq.gz NFD-2-2.fq.gz	fastq fastq	6680197200.0	22267324.0	NFD 2 1.fq.gz	0:150 1:150	A:1810744167;C:1526383805;G:1539949310;T:1803119918;N:0	150	150	1810744167	1526383805	1539949310	1803119918	0	SRX28842020	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
36235	36235	SRR33613680	SRX28842019	SRS25072222	SRP586119	PRJNA1263917	Danio rerio Transcriptome or Gene expression	PRJNA1263917	Other	Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.			Danio rerio	Danio rerio	strain:missing\|isolate:missing\|breed:missing\|cultivar:missing\|ecotype:missing\|age:7 day\|dev stage:Juvenile fish\|collection date:2024 04 16\|geo loc name:China: Hang Zhou\|sex:missing\|tissue:Whole body\|BioSampleModel:Model organism or animal									RNA seq of Danio rerio	NFD 1	NFD 1	Total RNA was extracted digested with DNase I and mRNA enriched. post fragmentation cDNA synthesis and library construction the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP586119		NFD-1-1.fq.gz NFD-1-2.fq.gz	fastq fastq	6587923800.0	21959746.0	NFD 1 1.fq.gz	0:150 1:150	A:1773646514;C:1516320091;G:1530275621;T:1767681574;N:0	150	150	1773646514	1516320091	1530275621	1767681574	0	SRX28842019	SRS25072222	SRA2131918	Yibin University\|Faculty of Quality Management and Inspection & Qua	Yibin University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2025-05-18	Multi-stage	Multi-stage	Trunk	Surface Structure
52250	52250	SRR9050625	SRX5827016	SRS4754830	SRP198298	PRJNA542704	Thyroid hormone regulates distinct paths to maturation in pigment cell lineages	GSE131136	Transcriptome Analysis	Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.	pubmed:31140974;pubmed:33933422		Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1	GSM3764572	tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue\|cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.\|treatment:Hypothyroid	Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1	Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.	sox10:Cre+ cells from post embryonic zebrafish trunk tissue	Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.	Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.	cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.\|treatment:Hypothyroid	GSM3764572	GSM3764572: Neural crest derived cells from hypothyroid juvenile zebrafish trunks biological replicate 1; Danio rerio; RNA Seq	GSM3764572		1	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP198298	dangling references:treat as unmapped	hypo7_possorted_genome_bam.bam	10X Genomics bam file	5078170983.0	89090719.0	GSM3764572 r1	0:57	A:1526791201;C:989860604;G:1192544480;T:1366270035;N:2704663	57		1526791201	989860604	1192544480	1366270035	2704663	SRX5827016	SRS4754830	SRA886020	GEO	Biology, University of Virginia	1	0.92899		0.25348		0.83571		0.48794		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-05-13	Multi-stage	Multi-stage	Trunk	Surface Structure
52256	52256	SRR9050619	SRX5827010	SRS4754824	SRP198298	PRJNA542704	Thyroid hormone regulates distinct paths to maturation in pigment cell lineages	GSE131136	Transcriptome Analysis	Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.	pubmed:31140974;pubmed:33933422		Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1	GSM3764566	tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue\|cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.\|treatment:Euthyroid	Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1	Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.	sox10:Cre+ cells from post embryonic zebrafish trunk tissue	Transgenic zebrafish Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.	Zebrafish were maintained at 28.5 °C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia rotifers enriched with TH free Algamac Aquafauna and bloodworms.	cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.\|treatment:Euthyroid	GSM3764566	GSM3764566: Neural crest derived cells from euthyroid post embryonic zebrafish trunks biological replicate 1; Danio rerio; RNA Seq	GSM3764566		1	10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP198298	dangling references:treat as unmapped	eu6_possorted_genome_bam.bam	10X Genomics bam file	5005233954.0	87811122.0	GSM3764566 r1	0:57	A:1531421605;C:966957285;G:1151579626;T:1352667292;N:2608146	57		1531421605	966957285	1151579626	1352667292	2608146	SRX5827010	SRS4754824	SRA886020	GEO	Biology, University of Virginia	1	0.92288		0.25231		0.83479		0.5014		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-05-13	Multi-stage	Multi-stage	Trunk	Surface Structure
60551	60551	SRR12354658	SRX8854020	SRS7115704	SRP274361	PRJNA649779	Unveiling the role of RAB13 localisation in angiogenesis	GSE155449	Other	Deciphering the complex biology of cell migration is key to understand human related disorders. During angiogenesis endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here we focused on RAB13 mRNA a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the three primeUTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis. Overall design: post identifying regions responsible for the localisation of RAB13 mRNA we used CRISPR/Cas9 technology with gRNAs targeting the three primeUTR of both human and zebrafish orthologues. We performed RNA seq experiments using RNA derived from control and mutant samples to 1 investigate whether potential off target sites were edited by CRISPR/Cas9 and 2 analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs 1x Wild type and 1x Homozygous RAB13 three primeUTR; Zebrafish 2x Wild type and 2x Homozygous RAB13 three primeUTR. Description of RAB13 three primeUTR mutations: Deletion of 190 nucleotides from Human RAB13 three primeUTR Deletion of 482 nucleotides from Zebrafish RAB13 three primeUTR	pubmed:32946121		HOM Zebrafish 2	GSM4704583	source name:Zebrafish embryo\|tissue:28 hpf embryo trunk\|genotype:Homozygous RAB13 3 prime UTR mutant\|passage:N/A	HOM Zebrafish 2	The stranded paired end RNA seq reads were quality assessed using FastQC v0.11.3 and FastQ Screen v0.9.2. The raw reads were processed with BBDuk part of the BBMap suite; v36.32 to trim the adapter sequences and low quality bases. Processed reads from the human derived samples were mapped against the reference assembly hg38 using STAR v2.7.2b with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32 whereas reads from the zebrafish derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99. Genome build: hg38 HUVEC samples; GRCz11 zebrafish samples Supplementary files format and content: bigWig files include RPKM values for each sample	Zebrafish embryo	HUVECs – cells were transfected with sgRNA Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates. post amplification cells were PCR genotyped and RNA was extracted from 1 non edited exemplar clone WT and 1 exemplar clone with bi allelic targeted deletion.	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	HUVECs were cultured in complete ECGM2 in gelatin coated dishes. Zebrafish were maintained and bred according to standard conditions.	tissue:28 hpf embryo trunk\|genotype:Homozygous RAB13 3 prime UTR mutant\|passage:N/A	GSM4704583	GSM4704583: HOM Zebrafish 2; Danio rerio; RNA Seq	GSM4704583		1	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	GEO Accession:GSM4704583	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP274361		HOM2_ZFISH_R1_001.fastq.gz HOM2_ZFISH_R2_001.fastq.gz	fastq fastq	6004982609.0	41535052.0	GSM4704583 r1	0:72.32 1:72.26	A:1491885198;C:1398869659;G:1358151351;T:1543048744;N:213027657	72	72	1491885198	1398869659	1358151351	1543048744	213027657	SRX8854020	SRS7115704	SRA1105789	GEO	University of Manchester	2	0.94327	0.92304	0.07649	0.07245	0.7123	0.71616	0.47152	0.47834	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2020-07-30	Multi-stage	Embryo	Trunk	Surface Structure
60552	60552	SRR12354657	SRX8854019	SRS7115703	SRP274361	PRJNA649779	Unveiling the role of RAB13 localisation in angiogenesis	GSE155449	Other	Deciphering the complex biology of cell migration is key to understand human related disorders. During angiogenesis endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here we focused on RAB13 mRNA a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the three primeUTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis. Overall design: post identifying regions responsible for the localisation of RAB13 mRNA we used CRISPR/Cas9 technology with gRNAs targeting the three primeUTR of both human and zebrafish orthologues. We performed RNA seq experiments using RNA derived from control and mutant samples to 1 investigate whether potential off target sites were edited by CRISPR/Cas9 and 2 analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs 1x Wild type and 1x Homozygous RAB13 three primeUTR; Zebrafish 2x Wild type and 2x Homozygous RAB13 three primeUTR. Description of RAB13 three primeUTR mutations: Deletion of 190 nucleotides from Human RAB13 three primeUTR Deletion of 482 nucleotides from Zebrafish RAB13 three primeUTR	pubmed:32946121		HOM Zebrafish 1	GSM4704582	source name:Zebrafish embryo\|tissue:28 hpf embryo trunk\|genotype:Homozygous RAB13 3 prime UTR mutant\|passage:N/A	HOM Zebrafish 1	The stranded paired end RNA seq reads were quality assessed using FastQC v0.11.3 and FastQ Screen v0.9.2. The raw reads were processed with BBDuk part of the BBMap suite; v36.32 to trim the adapter sequences and low quality bases. Processed reads from the human derived samples were mapped against the reference assembly hg38 using STAR v2.7.2b with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32 whereas reads from the zebrafish derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99. Genome build: hg38 HUVEC samples; GRCz11 zebrafish samples Supplementary files format and content: bigWig files include RPKM values for each sample	Zebrafish embryo	HUVECs – cells were transfected with sgRNA Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates. post amplification cells were PCR genotyped and RNA was extracted from 1 non edited exemplar clone WT and 1 exemplar clone with bi allelic targeted deletion.	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	HUVECs were cultured in complete ECGM2 in gelatin coated dishes. Zebrafish were maintained and bred according to standard conditions.	tissue:28 hpf embryo trunk\|genotype:Homozygous RAB13 3 prime UTR mutant\|passage:N/A	GSM4704582	GSM4704582: HOM Zebrafish 1; Danio rerio; RNA Seq	GSM4704582		1	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	GEO Accession:GSM4704582	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP274361		HOM1_ZFISH_R1_001.fastq.gz HOM1_ZFISH_R2_001.fastq.gz	fastq fastq	5929173021.0	41266794.0	GSM4704582 r1	0:71.87 1:71.81	A:1457916950;C:1380424836;G:1336027021;T:1506052175;N:248752039	71	71	1457916950	1380424836	1336027021	1506052175	248752039	SRX8854019	SRS7115703	SRA1105789	GEO	University of Manchester	2	0.94833	0.93844	0.07128	0.0686	0.71944	0.72153	0.46984	0.47347	35	35	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2020-07-30	Multi-stage	Embryo	Trunk	Surface Structure
60553	60553	SRR12354656	SRX8854018	SRS7115702	SRP274361	PRJNA649779	Unveiling the role of RAB13 localisation in angiogenesis	GSE155449	Other	Deciphering the complex biology of cell migration is key to understand human related disorders. During angiogenesis endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here we focused on RAB13 mRNA a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the three primeUTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis. Overall design: post identifying regions responsible for the localisation of RAB13 mRNA we used CRISPR/Cas9 technology with gRNAs targeting the three primeUTR of both human and zebrafish orthologues. We performed RNA seq experiments using RNA derived from control and mutant samples to 1 investigate whether potential off target sites were edited by CRISPR/Cas9 and 2 analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs 1x Wild type and 1x Homozygous RAB13 three primeUTR; Zebrafish 2x Wild type and 2x Homozygous RAB13 three primeUTR. Description of RAB13 three primeUTR mutations: Deletion of 190 nucleotides from Human RAB13 three primeUTR Deletion of 482 nucleotides from Zebrafish RAB13 three primeUTR	pubmed:32946121		WT Zebrafish 2	GSM4704581	source name:Zebrafish embryo\|tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	WT Zebrafish 2	The stranded paired end RNA seq reads were quality assessed using FastQC v0.11.3 and FastQ Screen v0.9.2. The raw reads were processed with BBDuk part of the BBMap suite; v36.32 to trim the adapter sequences and low quality bases. Processed reads from the human derived samples were mapped against the reference assembly hg38 using STAR v2.7.2b with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32 whereas reads from the zebrafish derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99. Genome build: hg38 HUVEC samples; GRCz11 zebrafish samples Supplementary files format and content: bigWig files include RPKM values for each sample	Zebrafish embryo	HUVECs – cells were transfected with sgRNA Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates. post amplification cells were PCR genotyped and RNA was extracted from 1 non edited exemplar clone WT and 1 exemplar clone with bi allelic targeted deletion.	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	HUVECs were cultured in complete ECGM2 in gelatin coated dishes. Zebrafish were maintained and bred according to standard conditions.	tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	GSM4704581	GSM4704581: WT Zebrafish 2; Danio rerio; RNA Seq	GSM4704581		1	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	GEO Accession:GSM4704581	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP274361		WT2_ZFISH_R1_001.fastq.gz WT2_ZFISH_R2_001.fastq.gz	fastq fastq	6290876399.0	42707622.0	GSM4704581 r1	0:73.69 1:73.61	A:1584257903;C:1497108723;G:1453835631;T:1638045619;N:117628523	73	73	1584257903	1497108723	1453835631	1638045619	117628523	SRX8854018	SRS7115702	SRA1105789	GEO	University of Manchester	2	0.94624	0.93483	0.08054	0.07777	0.69867	0.70126	0.4677	0.46596	75	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2020-07-30	Multi-stage	Embryo	Trunk	Surface Structure
60554	60554	SRR12354655	SRX8854017	SRS7115701	SRP274361	PRJNA649779	Unveiling the role of RAB13 localisation in angiogenesis	GSE155449	Other	Deciphering the complex biology of cell migration is key to understand human related disorders. During angiogenesis endothelial cells engage in coordinated migration events to form new blood vessels from parental counterparts. However while subcellular localisation of mRNAs and localised translation are fundamental steps between gene transcription and protein activity whether local regulation of gene expression controls the complex morphogenetic process of angiogenesis has never been addressed. Here we focused on RAB13 mRNA a transcript enriched at the leading front of many migratory cell types. We set out to delete regions in the three primeUTR of RAB13 mRNA responsible for its subcellular distribution in vitro and in vivo and to study its localised role during angiogenesis. Overall design: post identifying regions responsible for the localisation of RAB13 mRNA we used CRISPR/Cas9 technology with gRNAs targeting the three primeUTR of both human and zebrafish orthologues. We performed RNA seq experiments using RNA derived from control and mutant samples to 1 investigate whether potential off target sites were edited by CRISPR/Cas9 and 2 analyse the expression of potential RAB13 splicing variants. Samples analysed: HUVECs 1x Wild type and 1x Homozygous RAB13 three primeUTR; Zebrafish 2x Wild type and 2x Homozygous RAB13 three primeUTR. Description of RAB13 three primeUTR mutations: Deletion of 190 nucleotides from Human RAB13 three primeUTR Deletion of 482 nucleotides from Zebrafish RAB13 three primeUTR	pubmed:32946121		WT Zebrafish 1	GSM4704580	source name:Zebrafish embryo\|tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	WT Zebrafish 1	The stranded paired end RNA seq reads were quality assessed using FastQC v0.11.3 and FastQ Screen v0.9.2. The raw reads were processed with BBDuk part of the BBMap suite; v36.32 to trim the adapter sequences and low quality bases. Processed reads from the human derived samples were mapped against the reference assembly hg38 using STAR v2.7.2b with “–quantMode GeneCounts” option to obtain read count for each gene annotated in GENCODE v32 whereas reads from the zebrafish derived samples were mapped against the reference assembly GRCz11 and gene annotation from Ensembl v99. Genome build: hg38 HUVEC samples; GRCz11 zebrafish samples Supplementary files format and content: bigWig files include RPKM values for each sample	Zebrafish embryo	HUVECs – cells were transfected with sgRNA Cas9 ribonucleoproteins and a GFP expressing plasmid. GFP+ cells were harvested 48 hours later and single cell FACS sorted in 96 well plates. post amplification cells were PCR genotyped and RNA was extracted from 1 non edited exemplar clone WT and 1 exemplar clone with bi allelic targeted deletion.	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	HUVECs were cultured in complete ECGM2 in gelatin coated dishes. Zebrafish were maintained and bred according to standard conditions.	tissue:28 hpf embryo trunk\|genotype:Wild type\|passage:N/A	GSM4704580	GSM4704580: WT Zebrafish 1; Danio rerio; RNA Seq	GSM4704580		1	Zebrafish – zygote stage embryos were injected with sgRNA Cas9 ribonucleoproteins and grown to adult stages. Germline transmission of targeted deletion was performed by PCR and 1 desired founder animal F0 was identified. The F0 was outcrossed to Wt animals to generate F1 heterozygous animals. F1 animals were incrossed and the resulting offspring was grown 28 hours stage embryos. Heads were dissected for PCR genotyping and the trunks of 2 WT and 2 HOM embryos were processed for RNA extraction. RNA seq library prepared with TruSeq Stranded mRNA Illumina	GEO Accession:GSM4704580	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP274361		WT1_ZFISH_R1_001.fastq.gz WT1_ZFISH_R2_001.fastq.gz	fastq fastq	8044011744.0	54777035.0	GSM4704580 r1	0:73.46 1:73.39	A:2032870189;C:1897481528;G:1840068049;T:2099766774;N:173825204	73	73	2032870189	1897481528	1840068049	2099766774	173825204	SRX8854017	SRS7115701	SRA1105789	GEO	University of Manchester	2	0.94397	0.93722	0.0896	0.08658	0.70713	0.70871	0.46726	0.47109	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2020-07-30	Multi-stage	Embryo	Trunk	Surface Structure
66727	66727	SRR16494150	SRX12697149	SRS10647152	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		BPS1 3	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105138 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=6\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed	FRAS210076288 1r	FRAS210076288 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		BPS1_3_1.fq.gz BPS1_3_2.fq.gz	fastq fastq	7167849600.0	23892832.0	BPS1 3 1.fq.gz	0:150 1:150	A:1918014367;C:1678861019;G:1677677143;T:1893251281;N:45790	150	150	1918014367	1678861019	1677677143	1893251281	45790	SRX12697149	SRS10647152	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.95027	0.95031	0.10013	0.10018	0.67789	0.67771	0.45849	0.45672	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
66728	66728	SRR16494151	SRX12697148	SRS10647151	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		BPS1 2	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105137 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=5\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed	FRAS210076287 1r	FRAS210076287 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		BPS1_2_1.fq.gz BPS1_2_2.fq.gz	fastq fastq	7612619700.0	25375399.0	BPS1 2 1.fq.gz	0:150 1:150	A:2031729658;C:1792968404;G:1787711984;T:1999989075;N:220579	150	150	2031729658	1792968404	1787711984	1999989075	220579	SRX12697148	SRS10647151	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.95101	0.95113	0.09524	0.09456	0.68274	0.68318	0.45837	0.45319	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
66729	66729	SRR16494152	SRX12697147	SRS10647150	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		BPS1 1	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105136 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=4\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed	FRAS210076286 1r	FRAS210076286 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		BPS1_1_1.fq.gz BPS1_1_2.fq.gz	fastq fastq	6244935600.0	20816452.0	BPS1 1 1.fq.gz	0:150 1:150	A:1675323145;C:1456410435;G:1458522814;T:1654433698;N:245508	150	150	1675323145	1456410435	1458522814	1654433698	245508	SRX12697147	SRS10647150	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.94597	0.94597	0.10252	0.1028	0.67913	0.67963	0.4519	0.45424	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
66730	66730	SRR16494153	SRX12697146	SRS10647149	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		DMSO 3	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105135 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=3\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : DMSO exposed	FRAS210076285 1r	FRAS210076285 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		DMSO_3_1.fq.gz DMSO_3_2.fq.gz	fastq fastq	6977113200.0	23257044.0	DMSO 3 1.fq.gz	0:150 1:150	A:1886115659;C:1619020544;G:1612888187;T:1858808303;N:280507	150	150	1886115659	1619020544	1612888187	1858808303	280507	SRX12697146	SRS10647149	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.94817	0.94818	0.10571	0.10532	0.67957	0.6802	0.46251	0.46156	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
66731	66731	SRR16494154	SRX12697145	SRS10647148	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		DMSO 2	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105134 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=2\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : DMSO exposed	FRAS210076284 1r	FRAS210076284 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		DMSO_2_1.fq.gz DMSO_2_2.fq.gz	fastq fastq	6084760800.0	20282536.0	DMSO 2 1.fq.gz	0:150 1:150	A:1662685386;C:1398235089;G:1387347206;T:1636254391;N:238728	150	150	1662685386	1398235089	1387347206	1636254391	238728	SRX12697145	SRS10647148	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.94513	0.94552	0.12007	0.12016	0.67732	0.67698	0.46577	0.46663	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
66732	66732	SRR16494155	SRX12697144	SRS10647147	SRP342232	PRJNA772880	Bisphenol S affects zebrafish RNA seq analysis	PRJNA772880	Other	RNAseq data of 48 hpf zebrafish under bisphenol S		DMSO 1	RNA seq of zebrafish at 48 hpf in DMSO exposed	FKRO210105133 1A	isolate:AB type\|ecotype:AB type\|age:1 year\|dev stage:48 hpf\|sex:not applicable\|tissue:all body\|biomaterial provider:ecotoxicology of OUC\|ID:replicate=1\|BioSampleModel:Model organism or animal									RNA seq of zebrafish at 48 hpf : DMSO exposed	FRAS210076283 1r	FRAS210076283 1r	The first cDNA strand was synthesized in the m MulV reverse transcriptase system and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP342232		DMSO_1_1.fq.gz DMSO_1_2.fq.gz	fastq fastq	7313502000.0	24378340.0	DMSO 1 1.fq.gz	0:150 1:150	A:1980180330;C:1695610385;G:1686058673;T:1951359106;N:293506	150	150	1980180330	1695610385	1686058673	1951359106	293506	SRX12697144	SRS10647147	SRA1313827	Ocean University of China\|College of Marine Life Sciences	Ocean University of China	2	0.94872	0.94801	0.10719	0.10597	0.68221	0.68162	0.47058	0.46764	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2021-10-20	Multi-stage	Multi-stage	Trunk	Surface Structure
72477	72477	SRR22577926	SRX18540948	SRS16005333	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		SM3 sample RNA42	GSM6806702	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:SM\|treatment:Stress Metabolites at 27C	SM3 sample RNA42	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:SM\|treatment:Stress Metabolites at 27C	GSM6806702	GSM6806702: SM3 sample RNA42; Danio rerio; RNA Seq	GSM6806702 r1	GSM6806702	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0041L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0041L01_2.fastq.gz	fastq fastq	3476829400.0	34768294.0	GSM6806702 r1	0:50 1:50	A:938556753;C:788469231;G:822145048;T:927563690;N:94678	50	50	938556753	788469231	822145048	927563690	94678	SRX18540948	SRS16005333	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95691	0.96146	0.10137	0.10597	0.73734	0.73996	0.51422	0.51046	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72478	72478	SRR22577927	SRX18540947	SRS16005332	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		C3 sample RNA37	GSM6806701	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	C3 sample RNA37	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	GSM6806701	GSM6806701: C3 sample RNA37; Danio rerio; RNA Seq	GSM6806701 r1	GSM6806701	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0012L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0012L01_2.fastq.gz	fastq fastq	3115511600.0	31155116.0	GSM6806701 r1	0:50 1:50	A:818169661;C:736800852;G:743832124;T:816625526;N:83437	50	50	818169661	736800852	743832124	816625526	83437	SRX18540947	SRS16005332	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95909	0.9622	0.08549	0.08662	0.72174	0.72216	0.47764	0.47929	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72479	72479	SRR22577928	SRX18540946	SRS16005331	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS3 sample RNA36	GSM6806700	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	TS3 sample RNA36	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	GSM6806700	GSM6806700: TS3 sample RNA36; Danio rerio; RNA Seq	GSM6806700 r1	GSM6806700	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0011L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0011L01_2.fastq.gz	fastq fastq	4015833000.0	40158330.0	GSM6806700 r1	0:50 1:50	A:1048452902;C:957562374;G:965130701;T:1044578904;N:108119	50	50	1048452902	957562374	965130701	1044578904	108119	SRX18540946	SRS16005331	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.96228	0.9654	0.07673	0.07871	0.71565	0.71699	0.47598	0.48696	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72480	72480	SRR22577929	SRX18540945	SRS16005330	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS+SM3 sample RNA35	GSM6806699	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	TS+SM3 sample RNA35	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	GSM6806699	GSM6806699: TS+SM3 sample RNA35; Danio rerio; RNA Seq	GSM6806699 r1	GSM6806699	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0010L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0010L01_2.fastq.gz	fastq fastq	2689361200.0	26893612.0	GSM6806699 r1	0:50 1:50	A:714380354;C:630443184;G:634772606;T:709693436;N:71620	50	50	714380354	630443184	634772606	709693436	71620	SRX18540945	SRS16005330	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95508	0.96036	0.11483	0.11626	0.72464	0.72512	0.50789	0.50728	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72481	72481	SRR22577933	SRX18540944	SRS16005329	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		C2 sample RNA12	GSM6806698	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	C2 sample RNA12	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	GSM6806698	GSM6806698: C2 sample RNA12; Danio rerio; RNA Seq	GSM6806698 r1	GSM6806698	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0009L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0009L01_2.fastq.gz	fastq fastq	3600938900.0	36009389.0	GSM6806698 r1	0:50 1:50	A:947323197;C:850773040;G:856712191;T:946032751;N:97721	50	50	947323197	850773040	856712191	946032751	97721	SRX18540944	SRS16005329	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95605	0.96282	0.11507	0.11791	0.73667	0.73738	0.51713	0.5174	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72482	72482	SRR22577930	SRX18540943	SRS16005328	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		SM2 sample RNA10	GSM6806697	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:SM\|treatment:Stress Metabolites at 27C	SM2 sample RNA10	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:SM\|treatment:Stress Metabolites at 27C	GSM6806697	GSM6806697: SM2 sample RNA10; Danio rerio; RNA Seq	GSM6806697 r1	GSM6806697	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_2.fastq.gz	fastq fastq	2826043300.0	28260433.0	GSM6806697 r1	0:50 1:50	A:759619748;C:653720748;G:665257649;T:747369546;N:75609	50	50	759619748	653720748	665257649	747369546	75609	SRX18540943	SRS16005328	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95699	0.9614	0.09422	0.09721	0.73079	0.73241	0.48945	0.49521	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72483	72483	SRR22577931	SRX18540942	SRS16005327	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS+SM2 sample RNA9	GSM6806696	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	TS+SM2 sample RNA9	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	GSM6806696	GSM6806696: TS+SM2 sample RNA9; Danio rerio; RNA Seq	GSM6806696 r1	GSM6806696	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0007L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0007L01_2.fastq.gz	fastq fastq	3000657500.0	30006575.0	GSM6806696 r1	0:50 1:50	A:796059736;C:686227472;G:732263299;T:786033681;N:73312	50	50	796059736	686227472	732263299	786033681	73312	SRX18540942	SRS16005327	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95934	0.96295	0.08991	0.09091	0.74462	0.74424	0.48055	0.49465	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72484	72484	SRR22577932	SRX18540941	SRS16005326	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS2 sample RNA7	GSM6806695	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	TS2 sample RNA7	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	GSM6806695	GSM6806695: TS2 sample RNA7; Danio rerio; RNA Seq	GSM6806695 r1	GSM6806695	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0005L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0005L01_2.fastq.gz	fastq fastq	2782782000.0	27827820.0	GSM6806695 r1	0:50 1:50	A:748478002;C:640727379;G:651947739;T:741552359;N:76521	50	50	748478002	640727379	651947739	741552359	76521	SRX18540941	SRS16005326	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95766	0.96118	0.08698	0.08838	0.74231	0.74282	0.49457	0.48485	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72485	72485	SRR22577934	SRX18540940	SRS16005325	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS1 sample RNA6	GSM6806694	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	TS1 sample RNA6	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS\|treatment:Fresh medium with repeated heat stress	GSM6806694	GSM6806694: TS1 sample RNA6; Danio rerio; RNA Seq	GSM6806694 r1	GSM6806694	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0004L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0004L01_2.fastq.gz	fastq fastq	3939313200.0	39393132.0	GSM6806694 r1	0:50 1:50	A:1060730800;C:904303497;G:928318245;T:1045853002;N:107656	50	50	1060730800	904303497	928318245	1045853002	107656	SRX18540940	SRS16005325	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95569	0.96038	0.08993	0.09123	0.74377	0.74446	0.46546	0.49016	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72486	72486	SRR22577935	SRX18540939	SRS16005324	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		TS+SM1 sample RNA5	GSM6806693	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	TS+SM1 sample RNA5	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:TS+SM\|treatment:Stress Metabolites with repeated heat stress	GSM6806693	GSM6806693: TS+SM1 sample RNA5; Danio rerio; RNA Seq	GSM6806693 r1	GSM6806693	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_2_12030WK0003L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_2_12030WK0003L01_2.fastq.gz	fastq fastq	8000459900.0	80004599.0	GSM6806693 r1	0:50 1:50	A:2083773111;C:1806672672;G:2034786557;T:2075008672;N:218888	50	50	2083773111	1806672672	2034786557	2075008672	218888	SRX18540939	SRS16005324	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.9561	0.96287	0.07306	0.08163	0.76361	0.76329	0.48922	0.48488	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	Trunk	Surface Structure
72487	72487	SRR22577936	SRX18540938	SRS16005323	SRP412040	PRJNA910181	Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos	GSE220546	Transcriptome Analysis	Heat alters biology from molecular to ecological levels but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here we provide a comprehensive picture of the molecular signatures of this process by integrating multiomic and phenotypic data. In individual zebrafish embryos repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response extracellular signalling glycosaminoglycan/keratan sulphate and lipid metabolism. Consequently non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers inducing phenotypes comparable to those resulting from direct heat exposure but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line we independently confirm that the glycosaminoglycan biosynthesis related gene chs1 and the mucus glycoprotein gene prg4a functionally connected to the candidate stress metabolite classes sugars and phosphocholine are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers leading to further stress propagation within groups which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafi…	pubmed:37228511		C1 sample RNA3	GSM6806692	source name:1 dpf whole body embryos\|tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	C1 sample RNA3	The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1 to remove low quality reads polyG polyX and Illumina adapter sequences. Default parameters were used along with dup calc accuracy 3 trim poly g trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1 runMode alignReads quantMode TranscriptomeSAM GeneCounts outSAMtype BAM SortedByCoordinate outSAMunmapped None outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with " ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR which were used in DESeq2 for differential expression analysis.	1 dpf whole body embryos	Two temperature protocols were used either i a control constant temperature of 27°C or ii thermal stress protocol consisting of repeated heat stress with temperature fluctuations between 27 29 32 29 and 27°C with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites SM and incubated with their temperature protocols for 24 hours from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf i.e. post 24 hours of experimental treatment embryos were sampled by pools of 20 per condition and snap frozen at 80°C before total RNA extraction.	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.	Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27°C with 14:10 light:dark cycles. Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.	tissue:1 dpf whole body embryos\|genotype:Wild type Line: AB\|time:1 dpf group:C\|treatment:Control fresh medium at 27C	GSM6806692	GSM6806692: C1 sample RNA3; Danio rerio; RNA Seq	GSM6806692 r1	GSM6806692	1	Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP412040	loader:fastq load.py	211020_A00291_0393_AHM5V2DRXY_1_12030WK0002L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0002L01_2.fastq.gz	fastq fastq	3481198700.0	34811987.0	GSM6806692 r1	0:50 1:50	A:952025247;C:786684070;G:804510143;T:937885461;N:93779	50	50	952025247	786684070	804510143	937885461	93779	SRX18540938	SRS16005323	SRA1555908	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull	2	0.95315	0.95843	0.09382	0.09644	0.73795	0.73906	0.46673	0.48638	50	50	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United Kingdom	2022-12-08	Multi-stage	Multi-stage	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");;