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
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
69994,SRR19264376,SRX15324808,SRS13053424,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 50 µM   Replicate 4,GSM6165409,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA   Retene 50 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165409,GSM6165409: RNA   Retene 50 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165409 r1,GSM6165409,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret32_2.fq Ret32_1.fq,fastq fastq,4572659600.0,45726596.0,GSM6165409 r1,0:100 1:100,A:1232170294;C:1035171387;G:1089126986;T:1216190933;N:0,100,100,,,1232170294,1035171387,1089126986,1216190933,0,SRX15324808,SRS13053424,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.91127,,0.11591,,0.71317,,0.48482,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
69995,SRR19264377,SRX15324807,SRS13053423,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 50 µM   Replicate 3,GSM6165408,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA   Retene 50 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165408,GSM6165408: RNA   Retene 50 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165408 r1,GSM6165408,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret31_1.fq Ret31_2.fq,fastq fastq,4579737600.0,45797376.0,GSM6165408 r1,0:100 1:100,A:1219008458;C:1049195671;G:1093502477;T:1218030994;N:0,100,100,,,1219008458,1049195671,1093502477,1218030994,0,SRX15324807,SRS13053423,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93002,,0.08752,,0.7094,,0.493,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
69996,SRR19264378,SRX15324806,SRS13053422,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 50 µM   Replicate 2,GSM6165407,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA   Retene 50 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165407,GSM6165407: RNA   Retene 50 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165407 r1,GSM6165407,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret30_1.fq Ret30_2.fq,fastq fastq,4590395200.0,45903952.0,GSM6165407 r1,0:100 1:100,A:1207114959;C:1061518436;G:1113201421;T:1208560384;N:0,100,100,,,1207114959,1061518436,1113201421,1208560384,0,SRX15324806,SRS13053422,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93837,,0.08052,,0.70542,,0.49074,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
69997,SRR19264379,SRX15324805,SRS13053421,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 50 µM   Replicate 1,GSM6165406,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA   Retene 50 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165406,GSM6165406: RNA   Retene 50 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165406 r1,GSM6165406,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret29_2.fq Ret29_1.fq,fastq fastq,4565893800.0,45658938.0,GSM6165406 r1,0:100 1:100,A:1216518504;C:1041975840;G:1092350073;T:1215049383;N:0,100,100,,,1216518504,1041975840,1092350073,1215049383,0,SRX15324805,SRS13053421,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93015,,0.0903,,0.71088,,0.49418,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
69998,SRR19264380,SRX15324804,SRS13053420,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 20 µM   Replicate 4,GSM6165405,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA   Retene 20 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165405,GSM6165405: RNA   Retene 20 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165405 r1,GSM6165405,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret28_2.fq Ret28_1.fq,fastq fastq,4605153200.0,46051532.0,GSM6165405 r1,0:100 1:100,A:1237345826;C:1045225477;G:1091001207;T:1231580690;N:0,100,100,,,1237345826,1045225477,1091001207,1231580690,0,SRX15324804,SRS13053420,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92128,,0.10244,,0.70524,,0.49879,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
69999,SRR19264381,SRX15324803,SRS13053419,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 20 µM   Replicate 3,GSM6165404,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA   Retene 20 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165404,GSM6165404: RNA   Retene 20 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165404 r1,GSM6165404,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret27_2.fq Ret27_1.fq,fastq fastq,4596933800.0,45969338.0,GSM6165404 r1,0:100 1:100,A:1227576643;C:1047500037;G:1096955088;T:1224902032;N:0,100,100,,,1227576643,1047500037,1096955088,1224902032,0,SRX15324803,SRS13053419,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92878,,0.09222,,0.70544,,0.49805,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70000,SRR19264382,SRX15324802,SRS13053418,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 20 µM   Replicate 2,GSM6165403,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA   Retene 20 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165403,GSM6165403: RNA   Retene 20 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165403 r1,GSM6165403,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret26_1.fq Ret26_2.fq,fastq fastq,4596114400.0,45961144.0,GSM6165403 r1,0:100 1:100,A:1220023927;C:1054918236;G:1104509767;T:1216662470;N:0,100,100,,,1220023927,1054918236,1104509767,1216662470,0,SRX15324802,SRS13053418,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92714,,0.08942,,0.70834,,0.48781,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70001,SRR19264383,SRX15324801,SRS13053417,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 20 µM   Replicate 1,GSM6165402,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA   Retene 20 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165402,GSM6165402: RNA   Retene 20 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165402 r1,GSM6165402,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret25_1.fq Ret25_2.fq,fastq fastq,4588797000.0,45887970.0,GSM6165402 r1,0:100 1:100,A:1221596882;C:1049586741;G:1105734392;T:1211878985;N:0,100,100,,,1221596882,1049586741,1105734392,1211878985,0,SRX15324801,SRS13053417,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92083,,0.08963,,0.70936,,0.48202,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70002,SRR19264384,SRX15324800,SRS13053416,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 8 µM   Replicate 4,GSM6165401,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA   Retene 8 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165401,GSM6165401: RNA   Retene 8 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165401 r1,GSM6165401,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret24_1.fq Ret24_2.fq,fastq fastq,4624156600.0,46241566.0,GSM6165401 r1,0:100 1:100,A:1205935971;C:1080155692;G:1125498382;T:1212566555;N:0,100,100,,,1205935971,1080155692,1125498382,1212566555,0,SRX15324800,SRS13053416,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94086,,0.0771,,0.70076,,0.48339,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70003,SRR19264385,SRX15324799,SRS13053415,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 8 µM   Replicate 3,GSM6165400,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA   Retene 8 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165400,GSM6165400: RNA   Retene 8 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165400 r1,GSM6165400,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret23_1.fq Ret23_2.fq,fastq fastq,4624324200.0,46243242.0,GSM6165400 r1,0:100 1:100,A:1218844152;C:1067729229;G:1115817781;T:1221933038;N:0,100,100,,,1218844152,1067729229,1115817781,1221933038,0,SRX15324799,SRS13053415,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93497,,0.07979,,0.70916,,0.49162,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70004,SRR19264386,SRX15324798,SRS13053414,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 8 µM   Replicate 2,GSM6165399,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA   Retene 8 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165399,GSM6165399: RNA   Retene 8 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165399 r1,GSM6165399,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret22_1.fq Ret22_2.fq,fastq fastq,4630355600.0,46303556.0,GSM6165399 r1,0:100 1:100,A:1234125157;C:1058827735;G:1103596542;T:1233806166;N:0,100,100,,,1234125157,1058827735,1103596542,1233806166,0,SRX15324798,SRS13053414,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92491,,0.09055,,0.71267,,0.49637,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70005,SRR19264387,SRX15324797,SRS13053413,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 8 µM   Replicate 1,GSM6165398,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA   Retene 8 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165398,GSM6165398: RNA   Retene 8 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165398 r1,GSM6165398,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret21_1.fq Ret21_2.fq,fastq fastq,4386431000.0,43864310.0,GSM6165398 r1,0:100 1:100,A:1164169162;C:1006840682;G:1048654370;T:1166766786;N:0,100,100,,,1164169162,1006840682,1048654370,1166766786,0,SRX15324797,SRS13053413,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93229,,0.08542,,0.71236,,0.49127,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70006,SRR19264388,SRX15324796,SRS13053412,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 3.2 µM   Replicate 4,GSM6165397,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA   Retene 3.2 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165397,GSM6165397: RNA   Retene 3.2 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165397 r1,GSM6165397,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret20_1.fq Ret20_2.fq,fastq fastq,4383419800.0,43834198.0,GSM6165397 r1,0:100 1:100,A:1156733640;C:1010925303;G:1051454425;T:1164306432;N:0,100,100,,,1156733640,1010925303,1051454425,1164306432,0,SRX15324796,SRS13053412,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93759,,0.0801,,0.70879,,0.49551,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70007,SRR19264389,SRX15324795,SRS13053411,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 3.2 µM   Replicate 3,GSM6165396,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA   Retene 3.2 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165396,GSM6165396: RNA   Retene 3.2 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165396 r1,GSM6165396,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret19_2.fq Ret19_1.fq,fastq fastq,4389521800.0,43895218.0,GSM6165396 r1,0:100 1:100,A:1162594360;C:1009534036;G:1049443810;T:1167949594;N:0,100,100,,,1162594360,1009534036,1049443810,1167949594,0,SRX15324795,SRS13053411,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93573,,0.08567,,0.70611,,0.48715,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70008,SRR19264390,SRX15324794,SRS13053410,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 3.2 µM   Replicate 2,GSM6165395,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA   Retene 3.2 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165395,GSM6165395: RNA   Retene 3.2 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165395 r1,GSM6165395,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret18_1.fq Ret18_2.fq,fastq fastq,4397887000.0,43978870.0,GSM6165395 r1,0:100 1:100,A:1163596419;C:1012807954;G:1054042174;T:1167440453;N:0,100,100,,,1163596419,1012807954,1054042174,1167440453,0,SRX15324794,SRS13053410,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9311,,0.09135,,0.70518,,0.49131,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70009,SRR19264391,SRX15324793,SRS13053409,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 3.2 µM   Replicate 1,GSM6165394,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA   Retene 3.2 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165394,GSM6165394: RNA   Retene 3.2 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165394 r1,GSM6165394,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret17_1.fq Ret17_2.fq,fastq fastq,4615185200.0,46151852.0,GSM6165394 r1,0:100 1:100,A:1209825639;C:1071817166;G:1115963072;T:1217579323;N:0,100,100,,,1209825639,1071817166,1115963072,1217579323,0,SRX15324793,SRS13053409,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94207,,0.07533,,0.70672,,0.49039,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70010,SRR19264392,SRX15324792,SRS13053408,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 1.28 µM   Replicate 4,GSM6165393,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA   Retene 1.28 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165393,GSM6165393: RNA   Retene 1.28 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165393 r1,GSM6165393,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret16_1.fq Ret16_2.fq,fastq fastq,4384911400.0,43849114.0,GSM6165393 r1,0:100 1:100,A:1170400515;C:1001704172;G:1042001905;T:1170804808;N:0,100,100,,,1170400515,1001704172,1042001905,1170804808,0,SRX15324792,SRS13053408,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92473,,0.09931,,0.70721,,0.48941,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70011,SRR19264393,SRX15324791,SRS13053407,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 1.28 µM   Replicate 3,GSM6165392,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA   Retene 1.28 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165392,GSM6165392: RNA   Retene 1.28 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165392 r1,GSM6165392,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret15_1.fq Ret15_2.fq,fastq fastq,4384128000.0,43841280.0,GSM6165392 r1,0:100 1:100,A:1175348660;C:998065234;G:1039750478;T:1170963628;N:0,100,100,,,1175348660,998065234,1039750478,1170963628,0,SRX15324791,SRS13053407,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92006,,0.10061,,0.71029,,0.49305,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70012,SRR19264394,SRX15324790,SRS13053406,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 1.28 µM   Replicate 2,GSM6165391,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA   Retene 1.28 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165391,GSM6165391: RNA   Retene 1.28 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165391 r1,GSM6165391,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret14_1.fq Ret14_2.fq,fastq fastq,4386590600.0,43865906.0,GSM6165391 r1,0:100 1:100,A:1162629143;C:1008431955;G:1048944378;T:1166585124;N:0,100,100,,,1162629143,1008431955,1048944378,1166585124,0,SRX15324790,SRS13053406,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92918,,0.09061,,0.70615,,0.48926,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70013,SRR19264395,SRX15324789,SRS13053405,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 1.28 µM   Replicate 1,GSM6165390,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA   Retene 1.28 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165390,GSM6165390: RNA   Retene 1.28 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165390 r1,GSM6165390,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret13_1.fq Ret13_2.fq,fastq fastq,4630946000.0,46309460.0,GSM6165390 r1,0:100 1:100,A:1222553747;C:1068043014;G:1111862124;T:1228487115;N:0,100,100,,,1222553747,1068043014,1111862124,1228487115,0,SRX15324789,SRS13053405,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9355,,0.08198,,0.71096,,0.49274,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70014,SRR19264396,SRX15324788,SRS13053404,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.512 µM   Replicate 4,GSM6165389,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA   Retene 0.512 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165389,GSM6165389: RNA   Retene 0.512 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165389 r1,GSM6165389,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret12_1.fq Ret12_2.fq,fastq fastq,4597887800.0,45978878.0,GSM6165389 r1,0:100 1:100,A:1211629239;C:1061362233;G:1107475120;T:1217421208;N:0,100,100,,,1211629239,1061362233,1107475120,1217421208,0,SRX15324788,SRS13053404,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93986,,0.07927,,0.70907,,0.47669,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70015,SRR19264397,SRX15324787,SRS13053403,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.512 µM   Replicate 3,GSM6165388,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA   Retene 0.512 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165388,GSM6165388: RNA   Retene 0.512 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165388 r1,GSM6165388,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret11_1.fq Ret11_2.fq,fastq fastq,4560391600.0,45603916.0,GSM6165388 r1,0:100 1:100,A:1204481849;C:1049709181;G:1091882975;T:1214317595;N:0,100,100,,,1204481849,1049709181,1091882975,1214317595,0,SRX15324787,SRS13053403,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93399,,0.0879,,0.70617,,0.48281,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70016,SRR19264398,SRX15324786,SRS13053402,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.512 µM   Replicate 2,GSM6165387,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA   Retene 0.512 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165387,GSM6165387: RNA   Retene 0.512 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165387 r1,GSM6165387,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret10_2.fq Ret10_1.fq,fastq fastq,4542900600.0,45429006.0,GSM6165387 r1,0:100 1:100,A:1189304147;C:1055343156;G:1099652770;T:1198600527;N:0,100,100,,,1189304147,1055343156,1099652770,1198600527,0,SRX15324786,SRS13053402,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93819,,0.07628,,0.712,,0.4832,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70017,SRR19264399,SRX15324785,SRS13053401,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.512 µM   Replicate 1,GSM6165386,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA   Retene 0.512 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165386,GSM6165386: RNA   Retene 0.512 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165386 r1,GSM6165386,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret9_1.fq Ret9_2.fq,fastq fastq,4554791000.0,45547910.0,GSM6165386 r1,0:100 1:100,A:1208091587;C:1047925998;G:1085454060;T:1213319355;N:0,100,100,,,1208091587,1047925998,1085454060,1213319355,0,SRX15324785,SRS13053401,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92696,,0.08964,,0.70725,,0.47678,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70018,SRR19264400,SRX15324784,SRS13053400,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.205 µM   Replicate 4,GSM6165385,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA   Retene 0.205 µM   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165385,GSM6165385: RNA   Retene 0.205 µM   Replicate 4; Danio rerio; RNA Seq,GSM6165385 r1,GSM6165385,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret8_1.fq Ret8_2.fq,fastq fastq,4790224600.0,47902246.0,GSM6165385 r1,0:100 1:100,A:1284827524;C:1090358436;G:1135298341;T:1279740299;N:0,100,100,,,1284827524,1090358436,1135298341,1279740299,0,SRX15324784,SRS13053400,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.91468,,0.10225,,0.70688,,0.48401,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70019,SRR19264401,SRX15324783,SRS13053399,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.205 µM   Replicate 3,GSM6165384,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA   Retene 0.205 µM   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165384,GSM6165384: RNA   Retene 0.205 µM   Replicate 3; Danio rerio; RNA Seq,GSM6165384 r1,GSM6165384,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret7_1.fq Ret7_2.fq,fastq fastq,4549850800.0,45498508.0,GSM6165384 r1,0:100 1:100,A:1208192098;C:1046598883;G:1088752462;T:1206307357;N:0,100,100,,,1208192098,1046598883,1088752462,1206307357,0,SRX15324783,SRS13053399,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92485,,0.08773,,0.71482,,0.4865,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70020,SRR19264402,SRX15324782,SRS13053398,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.205 µM   Replicate 2,GSM6165383,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA   Retene 0.205 µM   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165383,GSM6165383: RNA   Retene 0.205 µM   Replicate 2; Danio rerio; RNA Seq,GSM6165383 r1,GSM6165383,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret6_1.fq Ret6_2.fq,fastq fastq,4537342000.0,45373420.0,GSM6165383 r1,0:100 1:100,A:1199051958;C:1046776379;G:1091726768;T:1199786895;N:0,100,100,,,1199051958,1046776379,1091726768,1199786895,0,SRX15324782,SRS13053398,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92685,,0.08488,,0.70946,,0.4809,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70021,SRR19264403,SRX15324781,SRS13053397,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Retene 0.205 µM   Replicate 1,GSM6165382,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA   Retene 0.205 µM   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165382,GSM6165382: RNA   Retene 0.205 µM   Replicate 1; Danio rerio; RNA Seq,GSM6165382 r1,GSM6165382,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret5_1.fq Ret5_2.fq,fastq fastq,4567176000.0,45671760.0,GSM6165382 r1,0:100 1:100,A:1207574600;C:1052993527;G:1095598503;T:1211009370;N:0,100,100,,,1207574600,1052993527,1095598503,1211009370,0,SRX15324781,SRS13053397,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92733,,0.08445,,0.7083,,0.47655,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70022,SRR19264404,SRX15324780,SRS13053396,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Vehicle control   Replicate 4,GSM6165381,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA   Vehicle control   Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165381,GSM6165381: RNA   Vehicle control   Replicate 4; Danio rerio; RNA Seq,GSM6165381 r1,GSM6165381,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret4_1.fq Ret4_2.fq,fastq fastq,4553955200.0,45539552.0,GSM6165381 r1,0:100 1:100,A:1202023760;C:1052394121;G:1091476117;T:1208061202;N:0,100,100,,,1202023760,1052394121,1091476117,1208061202,0,SRX15324780,SRS13053396,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92839,,0.0842,,0.70812,,0.48512,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70023,SRR19264405,SRX15324779,SRS13053395,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Vehicle control   Replicate 3,GSM6165380,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA   Vehicle control   Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165380,GSM6165380: RNA   Vehicle control   Replicate 3; Danio rerio; RNA Seq,GSM6165380 r1,GSM6165380,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret3_1.fq Ret3_2.fq,fastq fastq,4786982600.0,47869826.0,GSM6165380 r1,0:100 1:100,A:1260496096;C:1108347336;G:1153576121;T:1264563047;N:0,100,100,,,1260496096,1108347336,1153576121,1264563047,0,SRX15324779,SRS13053395,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9294,,0.08138,,0.71045,,0.47542,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70024,SRR19264406,SRX15324778,SRS13053394,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Vehicle control   Replicate 2,GSM6165379,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA   Vehicle control   Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165379,GSM6165379: RNA   Vehicle control   Replicate 2; Danio rerio; RNA Seq,GSM6165379 r1,GSM6165379,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret2_1.fq Ret2_2.fq,fastq fastq,4546668600.0,45466686.0,GSM6165379 r1,0:100 1:100,A:1203655800;C:1046900520;G:1091124255;T:1204988025;N:0,100,100,,,1203655800,1046900520,1091124255,1204988025,0,SRX15324778,SRS13053394,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92452,,0.09064,,0.69796,,0.46741,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
70025,SRR19264407,SRX15324777,SRS13053393,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations  we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA   Vehicle control   Replicate 1,GSM6165378,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA   Vehicle control   Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0  0.205  0.512  1.28  3.2  8  20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf  placed in 96 well plates in buffered embryo medium  statically exposed to retene or vehicle control beginning at 6 hpf  gently shaken overnight on an orbital shaker at 235 rpm  and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165378,GSM6165378: RNA   Vehicle control   Replicate 1; Danio rerio; RNA Seq,GSM6165378 r1,GSM6165378,1,48 hpf larvae were pooled into groups of 9 fish each  briefly anesthetized on ice  and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at  80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription  end repaired  three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret1_1.fq Ret1_2.fq,fastq fastq,4541215400.0,45412154.0,GSM6165378 r1,0:100 1:100,A:1200249191;C:1047425766;G:1091774738;T:1201765705;N:0,100,100,,,1200249191,1047425766,1091774738,1201765705,0,SRX15324777,SRS13053393,SRA1422455,"Robert L. Tanguay, Environmental &amp; Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9255,,0.08609,,0.70816,,0.47434,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75422,SRR24526045,SRX20310276,SRS17634751,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Mutant R3,GSM7329932,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1b Knockout|geo loc name:missing|collection date:missing,Foxj1b Mutant R3,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1b Knockout,GSM7329932,GSM7329932: Foxj1b Mutant R3; Danio rerio; RNA Seq,GSM7329932 r1,GSM7329932,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,12-Foxj1bmutant-3-10th-July_1.fq.gz 12-Foxj1bmutant-3-10th-July_2.fq.gz,fastq fastq,5202490600.0,26012453.0,GSM7329932 r1,0:100 1:100,A:1429503691;C:1158094263;G:1156226015;T:1458666631;N:0,100,100,,,1429503691,1158094263,1156226015,1458666631,0,SRX20310276,SRS17634751,SRA1637502,NTNU,NTNU,2,0.92806,0.92958,0.14142,0.14152,0.65531,0.65589,0.47275,0.474,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75423,SRR24526046,SRX20310275,SRS17634750,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Control R3,GSM7329931,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1b Control R3,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329931,GSM7329931: Foxj1b Control R3; Danio rerio; RNA Seq,GSM7329931 r1,GSM7329931,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,11-Foxj1bControl-3-10th-July_2.fq.gz 11-Foxj1bControl-3-10th-July_1.fq.gz,fastq fastq,4930483600.0,24652418.0,GSM7329931 r1,0:100 1:100,A:1356590983;C:1095780487;G:1097696007;T:1380416123;N:0,100,100,,,1356590983,1095780487,1097696007,1380416123,0,SRX20310275,SRS17634750,SRA1637502,NTNU,NTNU,2,0.92963,0.9307,0.13338,0.13396,0.65287,0.6562,0.49045,0.49232,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75424,SRR24526047,SRX20310274,SRS17634749,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Mutant R3,GSM7329930,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1a Knockout|geo loc name:missing|collection date:missing,Foxj1a Mutant R3,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1a Knockout,GSM7329930,GSM7329930: Foxj1a Mutant R3; Danio rerio; RNA Seq,GSM7329930 r1,GSM7329930,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,10-Foxj1aMutant-3-10th-July_2.fq.gz 10-Foxj1aMutant-3-10th-July_1.fq.gz,fastq fastq,4981288800.0,24906444.0,GSM7329930 r1,0:100 1:100,A:1373561625;C:1104331750;G:1102720098;T:1400675327;N:0,100,100,,,1373561625,1104331750,1102720098,1400675327,0,SRX20310274,SRS17634749,SRA1637502,NTNU,NTNU,2,0.92985,0.93185,0.14333,0.14449,0.65494,0.65754,0.48439,0.48896,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75425,SRR24526048,SRX20310273,SRS17634748,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Control R3,GSM7329929,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1a Control R3,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329929,GSM7329929: Foxj1a Control R3; Danio rerio; RNA Seq,GSM7329929 r1,GSM7329929,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,9-Foxj1aControl-3-10th-July_2.fq.gz 9-Foxj1aControl-3-10th-July_1.fq.gz,fastq fastq,5110368000.0,25551840.0,GSM7329929 r1,0:100 1:100,A:1397327985;C:1145018965;G:1146983540;T:1421037510;N:0,100,100,,,1397327985,1145018965,1146983540,1421037510,0,SRX20310273,SRS17634748,SRA1637502,NTNU,NTNU,2,0.93452,0.93552,0.12859,0.12902,0.65587,0.65715,0.49515,0.49552,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75426,SRR24526049,SRX20310272,SRS17634746,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Mutant R2,GSM7329928,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1b Knockout|geo loc name:missing|collection date:missing,Foxj1b Mutant R2,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1b Knockout,GSM7329928,GSM7329928: Foxj1b Mutant R2; Danio rerio; RNA Seq,GSM7329928 r1,GSM7329928,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,8-Foxj1bmutant-2-30th-June_1.fq.gz 8-Foxj1bmutant-2-30th-June_2.fq.gz,fastq fastq,4886103400.0,24430517.0,GSM7329928 r1,0:100 1:100,A:1331170839;C:1099736133;G:1102504200;T:1352692228;N:0,100,100,,,1331170839,1099736133,1102504200,1352692228,0,SRX20310272,SRS17634746,SRA1637502,NTNU,NTNU,2,0.93144,0.93303,0.1297,0.13001,0.65729,0.6579,0.48133,0.48014,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75427,SRR24526050,SRX20310271,SRS17634747,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Control R2,GSM7329927,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1b Control R2,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329927,GSM7329927: Foxj1b Control R2; Danio rerio; RNA Seq,GSM7329927 r1,GSM7329927,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,7-Foxj1bControl-2-30th-June_1.fq.gz 7-Foxj1bControl-2-30th-June_2.fq.gz,fastq fastq,5195488400.0,25977442.0,GSM7329927 r1,0:100 1:100,A:1453273337;C:1132544398;G:1132925932;T:1476744733;N:0,100,100,,,1453273337,1132544398,1132925932,1476744733,0,SRX20310271,SRS17634747,SRA1637502,NTNU,NTNU,2,0.9295,0.93085,0.15558,0.15713,0.65817,0.65934,0.48475,0.48394,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75428,SRR24526051,SRX20310270,SRS17634742,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Mutant R2,GSM7329926,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1a Knockout|geo loc name:missing|collection date:missing,Foxj1a Mutant R2,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1a Knockout,GSM7329926,GSM7329926: Foxj1a Mutant R2; Danio rerio; RNA Seq,GSM7329926 r1,GSM7329926,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,6-Foxj1aMutant-2-30th-June_1.fq.gz 6-Foxj1aMutant-2-30th-June_2.fq.gz,fastq fastq,4965081400.0,24825407.0,GSM7329926 r1,0:100 1:100,A:1388358986;C:1082202358;G:1081680333;T:1412839723;N:0,100,100,,,1388358986,1082202358,1081680333,1412839723,0,SRX20310270,SRS17634742,SRA1637502,NTNU,NTNU,2,0.92786,0.92878,0.15512,0.15603,0.65719,0.65752,0.49169,0.48648,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75429,SRR24526052,SRX20310269,SRS17634744,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Control R2,GSM7329925,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1a Control R2,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329925,GSM7329925: Foxj1a Control R2; Danio rerio; RNA Seq,GSM7329925 r1,GSM7329925,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,5-Foxj1aControl-2-30th-June_1.fq.gz 5-Foxj1aControl-2-30th-June_2.fq.gz,fastq fastq,4958039400.0,24790197.0,GSM7329925 r1,0:100 1:100,A:1388012642;C:1078189151;G:1080159974;T:1411677633;N:0,100,100,,,1388012642,1078189151,1080159974,1411677633,0,SRX20310269,SRS17634744,SRA1637502,NTNU,NTNU,2,0.92573,0.92653,0.16139,0.16191,0.65512,0.65541,0.4936,0.49512,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75430,SRR24526053,SRX20310268,SRS17634745,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Mutant R1,GSM7329924,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1b Knockout|geo loc name:missing|collection date:missing,Foxj1b Mutant R1,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1b Knockout,GSM7329924,GSM7329924: Foxj1b Mutant R1; Danio rerio; RNA Seq,GSM7329924 r1,GSM7329924,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,4-Foxj1bmutant-1-23rd-June_2.fq.gz 4-Foxj1bmutant-1-23rd-June_1.fq.gz,fastq fastq,5196215800.0,25981079.0,GSM7329924 r1,0:100 1:100,A:1453336241;C:1131637096;G:1133451422;T:1477791041;N:0,100,100,,,1453336241,1131637096,1133451422,1477791041,0,SRX20310268,SRS17634745,SRA1637502,NTNU,NTNU,2,0.9253,0.92723,0.15725,0.15841,0.65825,0.65912,0.48693,0.48176,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75431,SRR24526054,SRX20310267,SRS17634743,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1b Control R1,GSM7329923,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1b Control R1,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329923,GSM7329923: Foxj1b Control R1; Danio rerio; RNA Seq,GSM7329923 r1,GSM7329923,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,3-Foxj1bControl-1-23rd-June_1.fq.gz 3-Foxj1bControl-1-23rd-June_2.fq.gz,fastq fastq,5211422000.0,26057110.0,GSM7329923 r1,0:100 1:100,A:1456847014;C:1135730718;G:1138159907;T:1480684361;N:0,100,100,,,1456847014,1135730718,1138159907,1480684361,0,SRX20310267,SRS17634743,SRA1637502,NTNU,NTNU,2,0.9269,0.929,0.15464,0.15555,0.6594,0.66009,0.49015,0.48924,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75432,SRR24526055,SRX20310266,SRS17634741,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Mutant R1,GSM7329922,,source name:whole embryo|tissue:whole embryo|genotype:Foxj1a Knockout|geo loc name:missing|collection date:missing,Foxj1a Mutant R1,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Foxj1a Knockout,GSM7329922,GSM7329922: Foxj1a Mutant R1; Danio rerio; RNA Seq,GSM7329922 r1,GSM7329922,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,2-Foxj1aMutant-1-23rd-June_1.fq.gz 2-Foxj1aMutant-1-23rd-June_2.fq.gz,fastq fastq,4992459400.0,24962297.0,GSM7329922 r1,0:100 1:100,A:1395143614;C:1088437481;G:1088859898;T:1420018407;N:0,100,100,,,1395143614,1088437481,1088859898,1420018407,0,SRX20310266,SRS17634741,SRA1637502,NTNU,NTNU,2,0.92593,0.92739,0.15374,0.15452,0.65967,0.66095,0.48799,0.48995,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
75433,SRR24526056,SRX20310265,SRS17634740,SRP437444,PRJNA971920,Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons,GSE232397,Transcriptome Analysis,Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.,,pubmed:38271330,,Foxj1a Control R1,GSM7329921,,source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing,Foxj1a Control R1,In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts,whole embryo,,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI’s DNBSEQTM Technology.,Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C  14/10 light/dark cycle.,tissue:whole embryo|genotype:Wild Type,GSM7329921,GSM7329921: Foxj1a Control R1; Danio rerio; RNA Seq,GSM7329921 r1,GSM7329921,1,To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4°C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700μL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30μL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP437444,,,1-Foxj1aControl-1-23rd-June_1.fq.gz 1-Foxj1aControl-1-23rd-June_2.fq.gz,fastq fastq,4972894800.0,24864474.0,GSM7329921 r1,0:100 1:100,A:1386197977;C:1088117929;G:1090190808;T:1408388086;N:0,100,100,,,1386197977,1088117929,1090190808,1408388086,0,SRX20310265,SRS17634740,SRA1637502,NTNU,NTNU,2,0.9288,0.93042,0.15075,0.15148,0.66085,0.66344,0.49699,0.49109,100,100,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2023-05-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures