metadata: run_metadata: 138 rows where devstage_curation = "Multi-stage" and tissue_curation

138 rows where devstage_curation = "Multi-stage" and tissue_curation_coarse = "Surface Structure"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	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
25298	25298	SRR25764100	SRX21486771	SRS18719071	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf itgb4+ embryonic basal precursors rep2	GSM7734878	tissue:epidermal cells\|cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry\|geo loc name:missing\|collection date:missing	1 dpf itgb4+ embryonic basal precursors rep2	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry	GSM7734878	GSM7734878: 1 dpf itgb4+ embryonic basal precursors rep2; Danio rerio; RNA Seq	GSM7734878 r1	GSM7734878	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		itgb4mcherry_2_S229_R1_001.fastq.gz itgb4mcherry_2_S229_R2_001.fastq.gz	fastq fastq	6040245600.0	15100614.0	GSM7734878 r1	0:200 1:200	A:1588346322;C:1356558310;G:1524614760;T:1569583583;N:1142625	200	200	1588346322	1356558310	1524614760	1569583583	1142625	SRX21486771	SRS18719071	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.0156	0.0191	0.00074	0.00093	0.99024	0.99088	0.47058	0.47838	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25299	25299	SRR25764101	SRX21486770	SRS18719070	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf itgb4+ embryonic basal precursors rep1	GSM7734877	tissue:epidermal cells\|cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry\|geo loc name:missing\|collection date:missing	1 dpf itgb4+ embryonic basal precursors rep1	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic epidermal basal cells\|genotype:Tgitgb4:mcherry	GSM7734877	GSM7734877: 1 dpf itgb4+ embryonic basal precursors rep1; Danio rerio; RNA Seq	GSM7734877 r1	GSM7734877	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		itgb4mcherry_1_S20_R1_001.fastq.gz itgb4mcherry_1_S20_R2_001.fastq.gz	fastq fastq	7055215600.0	17638039.0	GSM7734877 r1	0:200 1:200	A:1894635584;C:1556854856;G:1769420212;T:1825520802;N:8784146	200	200	1894635584	1556854856	1769420212	1825520802	8784146	SRX21486770	SRS18719070	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01135	0.01881	0.00043	0.00016	0.9932	0.99543	0.46234	0.43106	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25300	25300	SRR25764102	SRX21486769	SRS18719069	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf krt4+ embryonic periderm cells rep2	GSM7734876	tissue:epidermal cells\|cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp\|geo loc name:missing\|collection date:missing	1 dpf krt4+ embryonic periderm cells rep2	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp	GSM7734876	GSM7734876: 1 dpf krt4+ embryonic periderm cells rep2; Danio rerio; RNA Seq	GSM7734876 r1	GSM7734876	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		krt4cre-gfp_2_S4_R2_001.fastq.gz krt4cre-gfp_2_S4_R1_001.fastq.gz	fastq fastq	9439207600.0	23598019.0	GSM7734876 r1	0:200 1:200	A:2499982675;C:2086665360;G:2395002073;T:2454282285;N:3275207	200	200	2499982675	2086665360	2395002073	2454282285	3275207	SRX21486769	SRS18719069	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.44931	0.01877	0.02236	0.00115	0.80012	0.99032	0.45473	0.49453	200	200	B	T	mate2 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
25301	25301	SRR25764103	SRX21486768	SRS18719066	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193	1 dpf krt4+ embryonic periderm cells rep1	GSM7734875	tissue:epidermal cells\|cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp\|geo loc name:missing\|collection date:missing	1 dpf krt4+ embryonic periderm cells rep1	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:embryonic periderm cells\|genotype:Tgkrt4:creERt2;Olactb:loxP dsRed2 loxP egfp;cryaa:egfp	GSM7734875	GSM7734875: 1 dpf krt4+ embryonic periderm cells rep1; Danio rerio; RNA Seq	GSM7734875 r1	GSM7734875	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109		krt4cre-gfp_1_S19_R2_001.fastq.gz krt4cre-gfp_1_S19_R1_001.fastq.gz	fastq fastq	6119547200.0	15298868.0	GSM7734875 r1	0:200 1:200	A:1642059769;C:1349462427;G:1535937964;T:1584527048;N:7559992	200	200	1642059769	1349462427	1535937964	1584527048	7559992	SRX21486768	SRS18719066	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01112	0.01017	0.0003	0.00014	0.9931	0.99586	0.43605	0.40821	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Multi-stage	Multi-stage	Skin	Surface Structure
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
52209	52209	SRR8992787	SRX5771765	SRS4705624	SRP194294	PRJNA540521	Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores	GSE130526	Other	Understanding genetic and cellular bases of adult form remains a fundamental goal at the intersection of developmental and evolutionary biology. The skin pigment cells of vertebrates derived from embryonic neural crest are a useful system for elucidating mechanisms of fate specification pattern formation and how particular phenotypes impact organismal behavior and ecology. In a survey of Danio fishes including zebrafish Danio rerio we identified two populations of white pigment cells—leucophores—one of which arises by transdifferentiation of adult melanophores and another that develops from a yellow/orange xanthophore like progenitor. Single cell transcriptomic mutational chemical and ultrastructural analyses of zebrafish leucophores revealed cell type specific chemical compositions organelle configurations and genetic requirements. At the organismal level we identified distinct physiological responses of leucophores during environmental background matching and we show that leucophore complement influences behavior. Together our studies revealed new independently arisen pigment cell types and mechanisms of fate acquisition in zebrafish and illustrate how concerted analyses across hierarchical levels can provide insights into phenotypes and their evolution. Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform using zebrafish fin pigment cells FACs sorted for mCherry. For additional details see associated publication	pubmed:31138706	Zebrafish fin pigment cells	GSM3741778	tissue:Dorsal and anal fins\|cell type:pigment cells\|treatment:Untreated	Zebrafish fin pigment cells	Expression matrix files were generated using cellranger 10X genomics version 1.3.1 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. Genome build: GRCz11/danRer11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 1.3.1 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.	Dorsal and anal fins	Fins were amputated from fish expressing both pnp4a:palmmCherry and tyrp1b:palmmCherry. To approximately normalize capture of relevant cell types by quantity and improve the likelihood of recovering cells at intermediate states of differentiation we extracted distal dorsal fin regions 10 mm standard length SL; n=20 and proximal interstripe anal fin regions 14 mm SL; n=10. Tissue was enzymatically dissociated with Liberase 0.25 mg/mL in dPBS at 25°C for 15 min followed by manual trituration with a flame polished glass pipette for 5 min. Cell suspensions were then filtered through a 70 μm Nylon cell strainer to obtain a single cell suspension. Liberated cells were re suspended in 1% BSA / 5% FBS in dPBS and DAPI 0.1 μg/mL 15 min before FACS purification. All plastic and glass surfaces of cell contact were coated with 1% BSA in dPBS before to use. Prior to sorting for fluorescence levels single cells were isolated by sequentially gating cells according to their SSC A vs. FSC A FSC H vs FSC W and SSC H vs SSC W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. Cells from wild type zebrafish were used as negative control to determine gates for detection of mCherry and GFP fluorescence and then cells from transgenic fish were purified according to these gates. All samples were kept on ice except during Liberase incubation and then sorted chilled.	10X genomics V1 protocol following manufacturer recommendations.	Fish were maintained at 28.5C with 10 h : 14 h light:dark conditions. Larvae were reared with marine rotifers supplemented with Artemac Aquafauna followed by Artemia and flake food. Adults were maintained on Artemia and flake food. Fish stocks of Danio rerio: WTABb a derivative of inbred ABwp Tgtyrp1b:palm mCherrywp.rt11 Tgpnp4a:palmmCherrywp.rt10	cell type:pigment cells\|treatment:Untreated	GSM3741778	GSM3741778: Zebrafish fin pigment cells; Danio rerio; RNA Seq	GSM3741778		1	10X genomics V1 protocol following manufacturer recommendations.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP194294		leucophore_S9_L003_R2_001.fastq.gz leucophore_S9_L004_R1_001.fastq.gz	fastq fastq	424061944.0	10241510.0	GSM3741778 r1	0:26 1:57	A:119042142;C:89897538;G:98172861;T:116716009;N:233394	26	57	119042142	89897538	98172861	116716009	233394	SRX5771765	SRS4705624	SRA881136	GEO	Parichy Lab, Biology, University of Washington	1	0.33934		0.07693		0.8742		0.51425		57		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-04-30	Multi-stage	Multi-stage	Fin	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
58389	58389	SRR11486781	SRX8062812	SRS6431234	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1	GSM4455083	source name:whole fin\|date:2 dpa\|tissue:whole fin	RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	whole fin	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	date:2 dpa\|tissue:whole fin	GSM4455083	GSM4455083: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq	GSM4455083		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	GEO Accession:GSM4455083	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		JK-S8_S75_L008_R1_001.fastq.gz	fastq	2464411341.0	48321791.0	GSM4455083 r1	0:51 1:0	A:620643336;C:590840801;G:549905028;T:702758180;N:263996	51	0	620643336	590840801	549905028	702758180	263996	SRX8062812	SRS6431234	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91677		0.09917		0.71981		0.46761		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-04-06	Multi-stage	Multi-stage	Fin	Surface Structure
58390	58390	SRR11486780	SRX8062811	SRS6431233	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 2dpa; injured; batch 3; rep1	GSM4455082	source name:whole fin\|date:2 dpa\|tissue:whole fin	RNAseq; whole fin; 2dpa; injured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	whole fin	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	date:2 dpa\|tissue:whole fin	GSM4455082	GSM4455082: RNAseq; whole fin; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq	GSM4455082		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	GEO Accession:GSM4455082	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		JK-S6_S73_L008_R1_001.fastq.gz	fastq	2567417214.0	50341514.0	GSM4455082 r1	0:51 1:0	A:648888081;C:617286062;G:571907197;T:729086777;N:249097	51	0	648888081	617286062	571907197	729086777	249097	SRX8062811	SRS6431233	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91819		0.10483		0.72062		0.45077		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-04-06	Multi-stage	Multi-stage	Fin	Surface Structure
58391	58391	SRR11486779	SRX8062810	SRS6431232	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1	GSM4455081	source name:whole fin\|date:0 dpa\|tissue:whole fin	RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	whole fin	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	date:0 dpa\|tissue:whole fin	GSM4455081	GSM4455081: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq	GSM4455081		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	GEO Accession:GSM4455081	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		JK-S7_S74_L008_R1_001.fastq.gz	fastq	2644840467.0	51859617.0	GSM4455081 r1	0:51 1:0	A:676588053;C:621109147;G:581574642;T:765307978;N:260647	51	0	676588053	621109147	581574642	765307978	260647	SRX8062810	SRS6431232	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.89598		0.1281		0.71417		0.47147		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-04-06	Multi-stage	Multi-stage	Fin	Surface Structure
58392	58392	SRR11486778	SRX8062809	SRS6431231	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1	GSM4455080	source name:whole fin\|date:0 dpa\|tissue:whole fin	RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	whole fin	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	date:0 dpa\|tissue:whole fin	GSM4455080	GSM4455080: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq	GSM4455080		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA.	GEO Accession:GSM4455080	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		JK-S5_S72_L008_R1_001.fastq.gz	fastq	2412481254.0	47303554.0	GSM4455080 r1	0:51 1:0	A:616219239;C:570826024;G:531833820;T:693353914;N:248257	51	0	616219239	570826024	531833820	693353914	248257	SRX8062809	SRS6431231	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.90059		0.11572		0.72013		0.46152		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-04-06	Multi-stage	Multi-stage	Fin	Surface Structure
58393	58393	SRR11305419	SRX7910559	SRS6318068	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2	GSM4411419	source name:RNAseq; Fibroblast; 4dpi; injured\|time:4 dpa\|tissue:fibroblast\|genotype:wild type	RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; Fibroblast; 4dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:4 dpa\|tissue:fibroblast\|genotype:wild type	GSM4411419	GSM4411419: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2; Danio rerio; RNA Seq	GSM4411419		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411419	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		Fibro.RNAseq_injured_Regen_B2_S60_L008_R1_001.fastq.gz	fastq	3284939427.0	64410577.0	GSM4411419 r1	0:51 1:0	A:903305689;C:745606629;G:745227959;T:890156683;N:642467	51	0	903305689	745606629	745227959	890156683	642467	SRX7910559	SRS6318068	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.92145		0.11147		0.75091		0.47874		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58394	58394	SRR11305418	SRX7910558	SRS6318067	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1	GSM4411418	source name:RNAseq; Fibroblast; 4dpi; injured\|time:4 dpa\|tissue:fibroblast\|genotype:wild type	RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; Fibroblast; 4dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:4 dpa\|tissue:fibroblast\|genotype:wild type	GSM4411418	GSM4411418: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1; Danio rerio; RNA Seq	GSM4411418		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411418	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		Fibro.RNAseq_injured_Regen_A2_S59_L008_R1_001.fastq.gz	fastq	3208227063.0	62906413.0	GSM4411418 r1	0:51 1:0	A:889970085;C:720088600;G:719685444;T:877865381;N:617553	51	0	889970085	720088600	719685444	877865381	617553	SRX7910558	SRS6318067	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91814		0.12108		0.74704		0.51875		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58395	58395	SRR11305417	SRX7910557	SRS6318066	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2	GSM4411417	source name:RNAseq; Fibroblast; 0dpi; uninjured\|time:0 dpa\|tissue:fibroblast\|genotype:wild type	RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; Fibroblast; 0dpi; uninjured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:0 dpa\|tissue:fibroblast\|genotype:wild type	GSM4411417	GSM4411417: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2; Danio rerio; RNA Seq	GSM4411417		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411417	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		Fibro.RNAseq_uninjured_Uninj_B2_S58_L008_R1_001.fastq.gz	fastq	3779977251.0	74117201.0	GSM4411417 r1	0:51 1:0	A:1036587583;C:863955138;G:859693317;T:1019029136;N:712077	51	0	1036587583	863955138	859693317	1019029136	712077	SRX7910557	SRS6318066	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91762		0.12285		0.7683		0.47877		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58396	58396	SRR11305416	SRX7910556	SRS6318065	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1	GSM4411416	source name:RNAseq; Fibroblast; 0dpi; uninjured\|time:0 dpa\|tissue:fibroblast\|genotype:wild type	RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; Fibroblast; 0dpi; uninjured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:0 dpa\|tissue:fibroblast\|genotype:wild type	GSM4411416	GSM4411416: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA Seq	GSM4411416		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411416	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		Fibro.RNAseq_uninjured_Uninj_A2_S57_L008_R1_001.fastq.gz	fastq	3830264271.0	75103221.0	GSM4411416 r1	0:51 1:0	A:1040171853;C:881400891;G:878214685;T:1029746894;N:729948	51	0	1040171853	881400891	878214685	1029746894	729948	SRX7910556	SRS6318065	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.92032		0.09358		0.75771		0.4712		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58397	58397	SRR11305415	SRX7910555	SRS6318064	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 1dpa; injured; batch 2; rep3	GSM4411415	source name:RNAseq; whole fin; 1dpi; injured\|time:1 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 1dpa; injured; batch 2; rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 1dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:1 dpa\|tissue:whole fin\|genotype:wild type	GSM4411415	GSM4411415: RNAseq; whole fin; 1dpa; injured; batch 2; rep3; Danio rerio; RNA Seq	GSM4411415		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411415	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_injured_RNA_1dpa_A_S37_L004_R1_001.fastq.gz	fastq	2924051085.0	57334335.0	GSM4411415 r1	0:51 1:0	A:678403251;C:734140605;G:692166374;T:819274692;N:66163	51	0	678403251	734140605	692166374	819274692	66163	SRX7910555	SRS6318064	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.93427		0.06589		0.73866		0.45737		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58398	58398	SRR11305414	SRX7910554	SRS6318063	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 1dpa; injured; batch 2; rep2	GSM4411414	source name:RNAseq; whole fin; 1dpi; injured\|time:1 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 1dpa; injured; batch 2; rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 1dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:1 dpa\|tissue:whole fin\|genotype:wild type	GSM4411414	GSM4411414: RNAseq; whole fin; 1dpa; injured; batch 2; rep2; Danio rerio; RNA Seq	GSM4411414		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411414	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_injured_RNA_1dpa_B_S38_L004_R1_001.fastq.gz	fastq	3159176895.0	61944645.0	GSM4411414 r1	0:51 1:0	A:730026525;C:803379127;G:747179794;T:878521357;N:70092	51	0	730026525	803379127	747179794	878521357	70092	SRX7910554	SRS6318063	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.93516		0.07492		0.74602		0.46646		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58399	58399	SRR11305413	SRX7910553	SRS6318062	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 1dpa; injured; batch 2; rep1	GSM4411413	source name:RNAseq; whole fin; 1dpi; injured\|time:1 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 1dpa; injured; batch 2; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 1dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:1 dpa\|tissue:whole fin\|genotype:wild type	GSM4411413	GSM4411413: RNAseq; whole fin; 1dpa; injured; batch 2; rep1; Danio rerio; RNA Seq	GSM4411413		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411413	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_injured_RNA_1dpa_C_S39_L004_R1_001.fastq.gz	fastq	3053752296.0	59877496.0	GSM4411413 r1	0:51 1:0	A:705251373;C:775521263;G:724421121;T:848486693;N:71846	51	0	705251373	775521263	724421121	848486693	71846	SRX7910553	SRS6318062	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.9345		0.08171		0.74326		0.47043		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58400	58400	SRR11305412	SRX7910552	SRS6318061	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3	GSM4411412	source name:RNAseq; whole fin; 0dpi; uninjured\|time:0 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 0dpi; uninjured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:0 dpa\|tissue:whole fin\|genotype:wild type	GSM4411412	GSM4411412: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3; Danio rerio; RNA Seq	GSM4411412		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411412	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_uninjured_RNA_0dpa_B_S35_L004_R1_001.fastq.gz	fastq	3095170620.0	60689620.0	GSM4411412 r1	0:51 1:0	A:728515579;C:769711604;G:717419279;T:879450837;N:73321	51	0	728515579	769711604	717419279	879450837	73321	SRX7910552	SRS6318061	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91314		0.09911		0.72498		0.46006		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58401	58401	SRR11305411	SRX7910551	SRS6318060	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2	GSM4411411	source name:RNAseq; whole fin; 0dpi; uninjured\|time:0 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 0dpi; uninjured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:0 dpa\|tissue:whole fin\|genotype:wild type	GSM4411411	GSM4411411: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2; Danio rerio; RNA Seq	GSM4411411		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411411	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_uninjured_RNA_0dpa_C_S36_L004_R1_001.fastq.gz	fastq	2959811163.0	58035513.0	GSM4411411 r1	0:51 1:0	A:702000960;C:731163416;G:687625038;T:838953116;N:68633	51	0	702000960	731163416	687625038	838953116	68633	SRX7910551	SRS6318060	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91317		0.09909		0.7237		0.45771		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58402	58402	SRR11305410	SRX7910550	SRS6318059	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1	GSM4411410	source name:RNAseq; whole fin; 0dpi; uninjured\|time:0 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 0dpi; uninjured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:0 dpa\|tissue:whole fin\|genotype:wild type	GSM4411410	GSM4411410: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1; Danio rerio; RNA Seq	GSM4411410		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411410	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin1dpi.RNAseq_uninjured_RNA_0dpa_A_S34_L004_R1_001.fastq.gz	fastq	2850762963.0	55897313.0	GSM4411410 r1	0:51 1:0	A:675289993;C:707558547;G:662291002;T:805558844;N:64577	51	0	675289993	707558547	662291002	805558844	64577	SRX7910550	SRS6318059	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91288		0.10801		0.72165		0.46866		51		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58403	58403	SRR11305409	SRX7910549	SRS6318058	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 4dpa; injured; batch 1; rep2	GSM4411409	source name:RNAseq; whole fin; 4dpi; injured\|time:4 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 4dpa; injured; batch 1; rep2	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 4dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:4 dpa\|tissue:whole fin\|genotype:wild type	GSM4411409	GSM4411409: RNAseq; whole fin; 4dpa; injured; batch 1; rep2; Danio rerio; RNA Seq	GSM4411409		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411409	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin.RNAseq_injured_reg2.fastq.gz	fastq	2523651950.0	50473039.0	GSM4411409 r1	0:50	A:658848054;C:605884052;G:596099791;T:662690555;N:129498	50		658848054	605884052	596099791	662690555	129498	SRX7910549	SRS6318058	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.91959		0.07092		0.70717		0.45829		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	Surface Structure
58404	58404	SRR11305408	SRX7910548	SRS6318057	SRP252754	PRJNA612515	Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins	GSE146960	Other	Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa.	pubmed:32665240	RNAseq; whole fin; 4dpa; injured; batch 1; rep1	GSM4411408	source name:RNAseq; whole fin; 4dpi; injured\|time:4 dpa\|tissue:whole fin\|genotype:wild type	RNAseq; whole fin; 4dpa; injured; batch 1; rep1	RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. ATAC Seq reads were trimmed by Trim Galore 0.4.1 with q 15 and then mapped with bowtie22.2.5 with parameters very sensitive to zebrafish genome UCSC danRer10 refSeq annotation. The mapped reads were filtered by MAPQ greater than 30 by samtools v 1.5 and duplicated reads were removed by picard v 1.91. Bigwig files were generated by kentUtils. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph	RNAseq; whole fin; 4dpi; injured	For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank’s Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016 and homozygous evx1 knockout fish were used for evx1 libraries Schulte et al 2011. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.	time:4 dpa\|tissue:whole fin\|genotype:wild type	GSM4411408	GSM4411408: RNAseq; whole fin; 4dpa; injured; batch 1; rep1; Danio rerio; RNA Seq	GSM4411408		1	For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. For ATAC seq libraries biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged 3 month 12 month. Homozygous Evx1 knockout fish screened visually by jointless phenotype Borday et al. 2001 were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH Roche in Hank's Balanced Salt Solution Gibco stirring at 37°C for 2 hours collected in 15 minute increments then strained through a 70 μm nylon cell strainer Corning. Samples were quantitated for 100K live cells using the Countess Automated Cell Counter Thermo Fisher Scientific.Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. ATAC seq library preparation was performed as detailed in Buenrostro et al. 2013.	GEO Accession:GSM4411408	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP252754		WFin.RNAseq_injured_reg1.fastq.gz	fastq	2490897750.0	49817955.0	GSM4411408 r1	0:50	A:644634582;C:602186818;G:591877446;T:652072339;N:126565	50		644634582	602186818	591877446	652072339	126565	SRX7910548	SRS6318057	SRA1054723	GEO	Poss, Cell Biology, Duke University	1	0.92355		0.06175		0.71342		0.46396		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-13	Multi-stage	Multi-stage	Fin	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");;