rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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
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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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,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 &amp; 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
42197,SRR5485641,SRX2768777,SRS2152486,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,A 3.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,A 3.0.2,A 3.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz,fastq fastq,2072387100.0,20723871.0,HI.4079.001.Index 4.A R1.fastq.gz,0:100 1:0,A:539231555;C:478779687;G:466992364;T:587014266;N:369228,100,0,,,539231555,478779687,466992364,587014266,369228,SRX2768777,SRS2152486,SRA557480,Brandon University|Biology,Brandon University,1,0.94094,,0.13282,,0.67566,,0.46135,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42198,SRR5485640,SRX2768776,SRS2152485,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,B 3.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,B 3.5.2,B 3.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz,fastq fastq,2236492200.0,22364922.0,HI.4079.001.Index 5.B R1.fastq.gz,0:100 1:0,A:580646206;C:518191209;G:502712894;T:634542622;N:399269,100,0,,,580646206,518191209,502712894,634542622,399269,SRX2768776,SRS2152485,SRA557480,Brandon University|Biology,Brandon University,1,0.94188,,0.13073,,0.67653,,0.4635,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42199,SRR5485639,SRX2768775,SRS2152484,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,C 3.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,C 3.20.2,C 3.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz,fastq fastq,1979628000.0,19796280.0,HI.4079.001.Index 12.C R1.fastq.gz,0:100 1:0,A:519406228;C:453563284;G:442115002;T:564195493;N:347993,100,0,,,519406228,453563284,442115002,564195493,347993,SRX2768775,SRS2152484,SRA557480,Brandon University|Biology,Brandon University,1,0.93946,,0.14364,,0.6759,,0.46247,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42200,SRR5485638,SRX2768774,SRS2152483,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,D 3.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,D 3.0.14,D 3.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz,fastq fastq,1856095600.0,18560956.0,HI.4079.001.Index 19.D R1.fastq.gz,0:100 1:0,A:492424946;C:416504198;G:409645413;T:537196088;N:324955,100,0,,,492424946,416504198,409645413,537196088,324955,SRX2768774,SRS2152483,SRA557480,Brandon University|Biology,Brandon University,1,0.9288,,0.15497,,0.69232,,0.46842,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42201,SRR5485637,SRX2768773,SRS2152481,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,E 3.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,E 3.5.14,E 3.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz,fastq fastq,2936761500.0,29367615.0,HI.4079.001.Index 1.E R1.fastq.gz,0:100 1:0,A:762661816;C:675701333;G:661832769;T:836033713;N:531869,100,0,,,762661816,675701333,661832769,836033713,531869,SRX2768773,SRS2152481,SRA557480,Brandon University|Biology,Brandon University,1,0.93957,,0.12499,,0.67714,,0.4697,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2017-05-08,Undetermined,Multi-stage,Trunk,Surface Structure
42202,SRR5485636,SRX2768772,SRS2152480,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,F 3.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,F 3.20.14,F 3.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz,fastq fastq,2169884500.0,21698845.0,HI.4079.001.Index 3.F R1.fastq.gz,0:100 1:0,A:566808272;C:496620769;G:487930959;T:618144722;N:379778,100,0,,,566808272,496620769,487930959,618144722,379778,SRX2768772,SRS2152480,SRA557480,Brandon University|Biology,Brandon University,1,0.93678,,0.13131,,0.67635,,0.47972,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42203,SRR5485635,SRX2768771,SRS2152482,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,G 4.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,G 4.0.2,G 4.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz,fastq fastq,2008051800.0,20080518.0,HI.4079.001.Index 9.G R1.fastq.gz,0:100 1:0,A:518304309;C:466602325;G:455957803;T:566834696;N:352667,100,0,,,518304309,466602325,455957803,566834696,352667,SRX2768771,SRS2152482,SRA557480,Brandon University|Biology,Brandon University,1,0.94445,,0.12419,,0.68201,,0.46743,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42204,SRR5485634,SRX2768770,SRS2152479,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,H 4.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,H 4.5.2,H 4.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz,fastq fastq,1908097900.0,19080979.0,HI.4079.001.Index 8.H R1.fastq.gz,0:100 1:0,A:494318032;C:441931870;G:431477592;T:540030651;N:339755,100,0,,,494318032,441931870,431477592,540030651,339755,SRX2768770,SRS2152479,SRA557480,Brandon University|Biology,Brandon University,1,0.94216,,0.1306,,0.68195,,0.45834,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42205,SRR5485633,SRX2768769,SRS2152477,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,I 4.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,I 4.20.2,I 4.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz,fastq fastq,2059931100.0,20599311.0,HI.4079.001.Index 10.I R1.fastq.gz,0:100 1:0,A:536731862;C:475769707;G:462890515;T:584183211;N:355805,100,0,,,536731862,475769707,462890515,584183211,355805,SRX2768769,SRS2152477,SRA557480,Brandon University|Biology,Brandon University,1,0.93561,,0.13393,,0.68225,,0.46489,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42206,SRR5485632,SRX2768768,SRS2152478,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,J 4.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,J 4.0.14,J 4.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz,fastq fastq,2199504800.0,21995048.0,HI.4079.001.Index 11.J R1.fastq.gz,0:100 1:0,A:579625731;C:499663817;G:489173373;T:630657278;N:384601,100,0,,,579625731,499663817,489173373,630657278,384601,SRX2768768,SRS2152478,SRA557480,Brandon University|Biology,Brandon University,1,0.93523,,0.13836,,0.68655,,0.47839,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42207,SRR5485631,SRX2768767,SRS2152475,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,K 4.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,K 4.5.14,K 4.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz,fastq fastq,2154282200.0,21542822.0,HI.4079.001.Index 20.K R1.fastq.gz,0:100 1:0,A:563358732;C:494058898;G:482596638;T:613890813;N:377119,100,0,,,563358732,494058898,482596638,613890813,377119,SRX2768767,SRS2152475,SRA557480,Brandon University|Biology,Brandon University,1,0.93863,,0.12932,,0.67801,,0.46426,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42208,SRR5485630,SRX2768766,SRS2152476,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,L 4.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,L 4.20.14,L 4.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz,fastq fastq,2702515700.0,27025157.0,HI.4079.001.Index 22.L R1.fastq.gz,0:100 1:0,A:708045960;C:615042366;G:603133757;T:775807969;N:485648,100,0,,,708045960,615042366,603133757,775807969,485648,SRX2768766,SRS2152476,SRA557480,Brandon University|Biology,Brandon University,1,0.93316,,0.14421,,0.68915,,0.47027,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2017-05-08,Undetermined,Multi-stage,Trunk,Surface Structure
42209,SRR5485629,SRX2768765,SRS2152474,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,M 5.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,M 5.0.2,M 5.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz,fastq fastq,1999183400.0,19991834.0,HI.4079.001.Index 25.M R1.fastq.gz,0:100 1:0,A:526344986;C:456726468;G:447467581;T:568292150;N:352215,100,0,,,526344986,456726468,447467581,568292150,352215,SRX2768765,SRS2152474,SRA557480,Brandon University|Biology,Brandon University,1,0.9374,,0.14185,,0.67665,,0.47249,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42210,SRR5485628,SRX2768764,SRS2152473,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,N 5.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,N 5.5.2,N 5.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz,fastq fastq,2097386100.0,20973861.0,HI.4079.001.Index 21.N R1.fastq.gz,0:100 1:0,A:551586521;C:479609380;G:467572413;T:598246436;N:371350,100,0,,,551586521,479609380,467572413,598246436,371350,SRX2768764,SRS2152473,SRA557480,Brandon University|Biology,Brandon University,1,0.93984,,0.13949,,0.68219,,0.46921,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42211,SRR5485627,SRX2768763,SRS2152472,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,O 5.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,O 5.20.2,O 5.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz,fastq fastq,2003835800.0,20038358.0,HI.4079.001.Index 23.O R1.fastq.gz,0:100 1:0,A:529075084;C:456810826;G:444441300;T:573155538;N:353052,100,0,,,529075084,456810826,444441300,573155538,353052,SRX2768763,SRS2152472,SRA557480,Brandon University|Biology,Brandon University,1,0.93635,,0.15287,,0.67712,,0.45807,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42212,SRR5485626,SRX2768762,SRS2152471,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,P 5.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,P 5.0.14,P 5.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz,fastq fastq,1799355500.0,17993555.0,HI.4079.001.Index 27.P R1.fastq.gz,0:100 1:0,A:485156399;C:399414298;G:389730888;T:524733869;N:320046,100,0,,,485156399,399414298,389730888,524733869,320046,SRX2768762,SRS2152471,SRA557480,Brandon University|Biology,Brandon University,1,0.92813,,0.15749,,0.67943,,0.47424,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42213,SRR5485625,SRX2768761,SRS2152470,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,Q 5.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,Q 5.5.14,Q 5.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz,fastq fastq,2260494100.0,22604941.0,HI.4079.001.Index 2.Q R1.fastq.gz,0:100 1:0,A:602519260;C:506296484;G:495685951;T:655587703;N:404702,100,0,,,602519260,506296484,495685951,655587703,404702,SRX2768761,SRS2152470,SRA557480,Brandon University|Biology,Brandon University,1,0.92524,,0.14979,,0.6859,,0.47957,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42214,SRR5485624,SRX2768760,SRS2152469,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,R 5.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,R 5.20.14,R 5.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz,fastq fastq,1975297900.0,19752979.0,HI.4079.001.Index 13.R R1.fastq.gz,0:100 1:0,A:527732232;C:440160233;G:430962427;T:576091914;N:351094,100,0,,,527732232,440160233,430962427,576091914,351094,SRX2768760,SRS2152469,SRA557480,Brandon University|Biology,Brandon University,1,0.92785,,0.15864,,0.6814,,0.47773,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42215,SRR5485623,SRX2768759,SRS2152468,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,S 6.0.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,S 6.0.2,S 6.0.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz,fastq fastq,2690628500.0,26906285.0,HI.4079.001.Index 6.S R1.fastq.gz,0:100 1:0,A:713021693;C:609779787;G:594591832;T:772745072;N:490116,100,0,,,713021693,609779787,594591832,772745072,490116,SRX2768759,SRS2152468,SRA557480,Brandon University|Biology,Brandon University,1,0.93405,,0.15472,,0.68505,,0.45796,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42216,SRR5485622,SRX2768758,SRS2152466,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,T 6.5.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,T 6.5.2,T 6.5.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz,fastq fastq,1949043500.0,19490435.0,HI.4079.001.Index 15.T R1.fastq.gz,0:100 1:0,A:515794596;C:441198348;G:430323928;T:561379111;N:347517,100,0,,,515794596,441198348,430323928,561379111,347517,SRX2768758,SRS2152466,SRA557480,Brandon University|Biology,Brandon University,1,0.93579,,0.16207,,0.68473,,0.44993,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42217,SRR5485621,SRX2768757,SRS2152467,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,U 6.20.2,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,U 6.20.2,U 6.20.2,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz,fastq fastq,1754851900.0,17548519.0,HI.4079.001.Index 7.U R1.fastq.gz,0:100 1:0,A:464191451;C:397313933;G:387262108;T:505777499;N:306909,100,0,,,464191451,397313933,387262108,505777499,306909,SRX2768757,SRS2152467,SRA557480,Brandon University|Biology,Brandon University,1,0.93016,,0.16163,,0.68329,,0.47088,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42218,SRR5485620,SRX2768756,SRS2152463,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,V 6.0.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,V 6.0.14,V 6.0.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz,fastq fastq,2027423200.0,20274232.0,HI.4079.001.Index 18.V R1.fastq.gz,0:100 1:0,A:542440452;C:449399743;G:440389586;T:594839784;N:353635,100,0,,,542440452,449399743,440389586,594839784,353635,SRX2768756,SRS2152463,SRA557480,Brandon University|Biology,Brandon University,1,0.92441,,0.16974,,0.6842,,0.48209,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42219,SRR5485619,SRX2768755,SRS2152464,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,W 6.5.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,W 6.5.14,W 6.5.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz,fastq fastq,2139528300.0,21395283.0,HI.4079.001.Index 14.W R1.fastq.gz,0:100 1:0,A:569259910;C:478055273;G:469309420;T:622525486;N:378211,100,0,,,569259910,478055273,469309420,622525486,378211,SRX2768755,SRS2152464,SRA557480,Brandon University|Biology,Brandon University,1,0.92551,,0.15358,,0.68136,,0.47093,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
42220,SRR5485618,SRX2768754,SRS2152465,SRP105410,PRJNA384462,Danio rerio Transcriptome or Gene expression,PRJNA384462,Whole Genome Sequencing,5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.,,,,,X 6.20.14,,ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio Raw sequence reads,X 6.20.14,X 6.20.14,Illumina HiSeq read information to generate gene expression values,,,WGS,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP105410,,,HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz,fastq fastq,1768110400.0,17681104.0,HI.4079.001.Index 16.X R1.fastq.gz,0:100 1:0,A:472810124;C:392555880;G:382616900;T:519817796;N:309700,100,0,,,472810124,392555880,382616900,519817796,309700,SRX2768754,SRS2152465,SRA557480,Brandon University|Biology,Brandon University,1,0.92486,,0.16073,,0.69041,,0.48403,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Canada,2018-09-11,Undetermined,Multi-stage,Trunk,Surface Structure
43472,SRR6888831,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-003-Scar_R1.fastq.gz P2-CFin-Vent-003-Scar_R2.fastq.gz,fastq fastq,344793287.0,2269321.0,GSM3065988 r1,0:75.99 1:75.95,A:61565924;C:101344805;G:127059615;T:54785853;N:37090,75,75,,,61565924,101344805,127059615,54785853,37090,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00015,0.00029,0.00012,0.00017,0.99993,0.99977,0.33333,0.58823,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43473,SRR6888832,SRX3839382,SRS3086668,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P2 cfin vent Scar,GSM3065988,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P2 cfin vent Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065988,GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq,GSM3065988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz,fastq fastq,110701966.0,728490.0,GSM3065988 r2,0:75.99 1:75.97,A:19507928;C:32552811;G:40930271;T:17699467;N:11489,75,75,,,19507928,32552811,40930271,17699467,11489,SRX3839382,SRS3086668,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00021,0.0004,0.00015,0.00031,0.99991,0.99981,1.0,0.84615,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43474,SRR6888829,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-003-Scar_R2.fastq.gz P2-CFin-Dors-003-Scar_R1.fastq.gz,fastq fastq,537943644.0,3539989.0,GSM3065987 r1,0:75.99 1:75.97,A:94708808;C:157878001;G:198461680;T:86838061;N:57094,75,75,,,94708808,157878001,198461680,86838061,57094,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00016,0.00102,0.0001,0.00067,0.99995,0.99995,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43475,SRR6888830,SRX3839381,SRS3086670,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,P1 cfin dorsal Scar,GSM3065987,,tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,P1 cfin dorsal Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,primary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2,GSM3065987,GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq,GSM3065987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM3065987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz,fastq fastq,856597590.0,5637115.0,GSM3065987 r2,0:75.99 1:75.97,A:151359975;C:251587454;G:317011744;T:136549208;N:89209,75,75,,,151359975,251587454,317011744,136549208,89209,SRX3839381,SRS3086670,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00027,0.00065,0.00016,0.00039,0.99975,0.99951,0.29411,0.53658,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2018-03-23,Undetermined,Multi-stage,Fin,Surface Structure
43476,SRR6020446,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p01_R1.fastq.gz R5_sec_Trans_p01_R2.fastq.gz,fastq fastq,5031589058.0,33202740.0,GSM2776988 r1,0:75.79 1:75.75,A:1144328847;C:1211156155;G:1480041764;T:1195826451;N:235841,75,75,,,1144328847,1211156155,1480041764,1195826451,235841,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.11853,0.24563,0.10636,0.21925,0.96585,0.92555,0.49894,0.48592,75,75,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43477,SRR6020447,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p02_R2.fastq.gz R5_sec_Trans_p02_R1.fastq.gz,fastq fastq,5020749563.0,33189212.0,GSM2776988 r2,0:75.66 1:75.61,A:1271180542;C:1081665590;G:1257183505;T:1410487545;N:232381,75,75,,,1271180542,1081665590,1257183505,1410487545,232381,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.12477,0.33055,0.10671,0.26254,0.96773,0.90583,0.50071,0.48529,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43478,SRR6020448,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p03_R1.fastq.gz R5_sec_Trans_p03_R2.fastq.gz,fastq fastq,9930849737.0,65769125.0,GSM2776988 r3,0:75.49 1:75.50,A:2771601461;C:1594447174;G:1778419273;T:3786066213;N:315616,75,75,,,2771601461,1594447174,1778419273,3786066213,315616,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.31895,0.74881,0.28344,0.57326,0.96546,0.85234,0.4987,0.52017,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43479,SRR6020449,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p04_R1.fastq.gz R5_sec_Trans_p04_R2.fastq.gz,fastq fastq,7297925579.0,48343134.0,GSM2776988 r4,0:75.51 1:75.45,A:2157432534;C:1129186071;G:1200823243;T:2810444585;N:39146,75,75,,,2157432534,1129186071,1200823243,2810444585,39146,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.352,0.75293,0.31357,0.60441,0.95828,0.83885,0.50134,0.50535,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43480,SRR6020450,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p05_R2.fastq.gz R5_sec_Trans_p05_R1.fastq.gz,fastq fastq,13855953318.0,91804628.0,GSM2776988 r5,0:75.50 1:75.43,A:4146316683;C:2217362039;G:2391706547;T:5100492721;N:75328,75,75,,,4146316683,2217362039,2391706547,5100492721,75328,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.37449,0.68646,0.32985,0.54102,0.95347,0.849,0.49416,0.50708,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43481,SRR6020451,SRX3171493,SRS2501302,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Trans,GSM2776988,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Trans,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776988,GSM2776988: R5 sec Trans; Danio rerio; RNA Seq,GSM2776988,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776988,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Trans_p06_R1.fastq.gz R5_sec_Trans_p06_R2.fastq.gz,fastq fastq,9723577592.0,64415623.0,GSM2776988 r6,0:75.50 1:75.45,A:2835431401;C:1511580093;G:1616039076;T:3760473139;N:53883,75,75,,,2835431401,1511580093,1616039076,3760473139,53883,SRX3171493,SRS2501302,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.33655,0.77492,0.29229,0.58155,0.95978,0.8454,0.49546,0.51051,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43482,SRR6020440,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p01_R1.fastq.gz R5_sec_Scar_p01_R2.fastq.gz,fastq fastq,361194076.0,2376599.0,GSM2776987 r1,0:75.99 1:75.99,A:63932353;C:105212754;G:137339472;T:54692604;N:16893,75,75,,,63932353,105212754,137339472,54692604,16893,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,7e-05,0.00012,4e-05,9e-05,0.99993,0.99991,0.5,0.75,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43483,SRR6020441,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p02_R1.fastq.gz R5_sec_Scar_p02_R2.fastq.gz,fastq fastq,460055993.0,3027108.0,GSM2776987 r2,0:75.99 1:75.99,A:80579341;C:134185300;G:175364991;T:69904520;N:21841,75,75,,,80579341,134185300,175364991,69904520,21841,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,5e-05,2e-05,2e-05,0.0,0.99997,0.99997,0.0,1.0,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43484,SRR6020442,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p03_R1.fastq.gz R5_sec_Scar_p03_R2.fastq.gz,fastq fastq,466000423.0,3066554.0,GSM2776987 r3,0:75.98 1:75.98,A:81301391;C:136221817;G:177874701;T:70591092;N:11422,75,75,,,81301391,136221817,177874701,70591092,11422,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.0001,0.00016,8e-05,0.00011,0.99993,0.99987,0.0,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure
43485,SRR6020443,SRX3171492,SRS2501301,SRP116018,PRJNA399711,Whole organism clone tracing using single cell sequencing,GSE102990,Transcriptome Analysis,We present ScarTrace  a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast  we find that cells in the eyes  brain  and caudal tail fin arise from many embryonic progenitors  which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow  forebrain  hindbrain  left eye  right eye  left midbrain  right midbrain  and regenerated fin. For each cell  we provide libraries with transcritpome and with clonal information  respectively.,,pubmed:29590089,,R5 sec Scar,GSM2776987,,source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,R5 sec Scar,In scar libraries  first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files  with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID  plate and organ of origin.  Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID  plate  organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun  D. et al. Nature 525  251 255  2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.,secondary fin single cells,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,,cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6,GSM2776987,GSM2776987: R5 sec Scar; Danio rerio; RNA Seq,GSM2776987,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for independent scar and mRNA detection  Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters,GEO Accession:GSM2776987,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP116018,,,R5_sec_Scar_p04_R1.fastq.gz R5_sec_Scar_p04_R2.fastq.gz,fastq fastq,203843839.0,1341388.0,GSM2776987 r4,,,,,,,,,,,,SRX3171492,SRS2501301,SRA602108,GEO,"AVO, Hubrecht Institue",2,0.00013,0.00027,9e-05,0.00019,0.99995,0.99977,0.16666,0.66666,76,76,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,other_seq,scartrace,,Netherlands,2017-09-08,Undetermined,Multi-stage,Fin,Surface Structure