{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and experiment.platform = \"DNBSEQ\"", "rows": [[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.", null, "pubmed:38265193", null, "1 dpf itgb4+ embryonic basal precursors rep2", "GSM7734878", null, "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. 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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.", null, "pubmed:38265193", null, "1 dpf itgb4+ embryonic basal precursors rep1", "GSM7734877", null, "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. 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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.", null, "pubmed:38265193", null, "1 dpf krt4+ embryonic periderm cells rep2", "GSM7734876", null, "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. 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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.", null, "pubmed:38265193", null, "1 dpf krt4+ embryonic periderm cells rep1", "GSM7734875", null, "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. 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null, "Danio rerio", "Danio rerio", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "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, null, null, 1819443100, 1566081115, 1580525465, 1814007020, 0, "SRX28842022", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection & Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Danio rerio", "Danio rerio", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "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, null, null, 1794821611, 1541478212, 1552820105, 1788655972, 0, "SRX28842021", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection & Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Danio rerio", "Danio rerio", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "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, null, null, 1810744167, 1526383805, 1539949310, 1803119918, 0, "SRX28842020", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection & Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Danio rerio", "Danio rerio", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "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, null, null, 1773646514, 1516320091, 1530275621, 1767681574, 0, "SRX28842019", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection & Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 50 \u00b5M Replicate 4", "GSM6165409", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 50 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 50 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165409", "GSM6165409: RNA Retene 50 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1232170294, 1035171387, 1089126986, 1216190933, 0, "SRX15324808", "SRS13053424", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.91127, null, 0.11591, null, 0.71317, null, 0.48482, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 50 \u00b5M Replicate 3", "GSM6165408", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 50 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 50 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165408", "GSM6165408: RNA Retene 50 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1219008458, 1049195671, 1093502477, 1218030994, 0, "SRX15324807", "SRS13053423", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93002, null, 0.08752, null, 0.7094, null, 0.493, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 50 \u00b5M Replicate 2", "GSM6165407", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 50 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 50 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165407", "GSM6165407: RNA Retene 50 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1207114959, 1061518436, 1113201421, 1208560384, 0, "SRX15324806", "SRS13053422", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93837, null, 0.08052, null, 0.70542, null, 0.49074, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 50 \u00b5M Replicate 1", "GSM6165406", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 50 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 50 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165406", "GSM6165406: RNA Retene 50 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1216518504, 1041975840, 1092350073, 1215049383, 0, "SRX15324805", "SRS13053421", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93015, null, 0.0903, null, 0.71088, null, 0.49418, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 20 \u00b5M Replicate 4", "GSM6165405", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 20 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165405", "GSM6165405: RNA Retene 20 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1237345826, 1045225477, 1091001207, 1231580690, 0, "SRX15324804", "SRS13053420", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92128, null, 0.10244, null, 0.70524, null, 0.49879, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 20 \u00b5M Replicate 3", "GSM6165404", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 20 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165404", "GSM6165404: RNA Retene 20 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1227576643, 1047500037, 1096955088, 1224902032, 0, "SRX15324803", "SRS13053419", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92878, null, 0.09222, null, 0.70544, null, 0.49805, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 20 \u00b5M Replicate 2", "GSM6165403", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 20 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165403", "GSM6165403: RNA Retene 20 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1220023927, 1054918236, 1104509767, 1216662470, 0, "SRX15324802", "SRS13053418", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92714, null, 0.08942, null, 0.70834, null, 0.48781, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 20 \u00b5M Replicate 1", "GSM6165402", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 20 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 20 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165402", "GSM6165402: RNA Retene 20 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1221596882, 1049586741, 1105734392, 1211878985, 0, "SRX15324801", "SRS13053417", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92083, null, 0.08963, null, 0.70936, null, 0.48202, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 8 \u00b5M Replicate 4", "GSM6165401", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 8 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 8 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165401", "GSM6165401: RNA Retene 8 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1205935971, 1080155692, 1125498382, 1212566555, 0, "SRX15324800", "SRS13053416", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94086, null, 0.0771, null, 0.70076, null, 0.48339, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 8 \u00b5M Replicate 3", "GSM6165400", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 8 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 8 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165400", "GSM6165400: RNA Retene 8 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1218844152, 1067729229, 1115817781, 1221933038, 0, "SRX15324799", "SRS13053415", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93497, null, 0.07979, null, 0.70916, null, 0.49162, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 8 \u00b5M Replicate 2", "GSM6165399", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 8 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 8 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165399", "GSM6165399: RNA Retene 8 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1234125157, 1058827735, 1103596542, 1233806166, 0, "SRX15324798", "SRS13053414", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92491, null, 0.09055, null, 0.71267, null, 0.49637, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 8 \u00b5M Replicate 1", "GSM6165398", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 8 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 8 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165398", "GSM6165398: RNA Retene 8 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1164169162, 1006840682, 1048654370, 1166766786, 0, "SRX15324797", "SRS13053413", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93229, null, 0.08542, null, 0.71236, null, 0.49127, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 3.2 \u00b5M Replicate 4", "GSM6165397", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 3.2 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165397", "GSM6165397: RNA Retene 3.2 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1156733640, 1010925303, 1051454425, 1164306432, 0, "SRX15324796", "SRS13053412", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93759, null, 0.0801, null, 0.70879, null, 0.49551, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 3.2 \u00b5M Replicate 3", "GSM6165396", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 3.2 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165396", "GSM6165396: RNA Retene 3.2 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1162594360, 1009534036, 1049443810, 1167949594, 0, "SRX15324795", "SRS13053411", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93573, null, 0.08567, null, 0.70611, null, 0.48715, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 3.2 \u00b5M Replicate 2", "GSM6165395", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 3.2 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165395", "GSM6165395: RNA Retene 3.2 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1163596419, 1012807954, 1054042174, 1167440453, 0, "SRX15324794", "SRS13053410", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.9311, null, 0.09135, null, 0.70518, null, 0.49131, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 3.2 \u00b5M Replicate 1", "GSM6165394", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 3.2 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165394", "GSM6165394: RNA Retene 3.2 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1209825639, 1071817166, 1115963072, 1217579323, 0, "SRX15324793", "SRS13053409", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.94207, null, 0.07533, null, 0.70672, null, 0.49039, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 1.28 \u00b5M Replicate 4", "GSM6165393", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 1.28 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165393", "GSM6165393: RNA Retene 1.28 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1170400515, 1001704172, 1042001905, 1170804808, 0, "SRX15324792", "SRS13053408", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92473, null, 0.09931, null, 0.70721, null, 0.48941, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 1.28 \u00b5M Replicate 3", "GSM6165392", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 1.28 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165392", "GSM6165392: RNA Retene 1.28 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1175348660, 998065234, 1039750478, 1170963628, 0, "SRX15324791", "SRS13053407", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92006, null, 0.10061, null, 0.71029, null, 0.49305, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 1.28 \u00b5M Replicate 2", "GSM6165391", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 1.28 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165391", "GSM6165391: RNA Retene 1.28 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1162629143, 1008431955, 1048944378, 1166585124, 0, "SRX15324790", "SRS13053406", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92918, null, 0.09061, null, 0.70615, null, 0.48926, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 1.28 \u00b5M Replicate 1", "GSM6165390", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 1.28 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165390", "GSM6165390: RNA Retene 1.28 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1222553747, 1068043014, 1111862124, 1228487115, 0, "SRX15324789", "SRS13053405", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.9355, null, 0.08198, null, 0.71096, null, 0.49274, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.512 \u00b5M Replicate 4", "GSM6165389", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.512 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165389", "GSM6165389: RNA Retene 0.512 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1211629239, 1061362233, 1107475120, 1217421208, 0, "SRX15324788", "SRS13053404", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93986, null, 0.07927, null, 0.70907, null, 0.47669, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.512 \u00b5M Replicate 3", "GSM6165388", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.512 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165388", "GSM6165388: RNA Retene 0.512 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1204481849, 1049709181, 1091882975, 1214317595, 0, "SRX15324787", "SRS13053403", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93399, null, 0.0879, null, 0.70617, null, 0.48281, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.512 \u00b5M Replicate 2", "GSM6165387", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.512 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165387", "GSM6165387: RNA Retene 0.512 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1189304147, 1055343156, 1099652770, 1198600527, 0, "SRX15324786", "SRS13053402", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.93819, null, 0.07628, null, 0.712, null, 0.4832, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.512 \u00b5M Replicate 1", "GSM6165386", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.512 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165386", "GSM6165386: RNA Retene 0.512 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1208091587, 1047925998, 1085454060, 1213319355, 0, "SRX15324785", "SRS13053401", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92696, null, 0.08964, null, 0.70725, null, 0.47678, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.205 \u00b5M Replicate 4", "GSM6165385", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.205 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165385", "GSM6165385: RNA Retene 0.205 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1284827524, 1090358436, 1135298341, 1279740299, 0, "SRX15324784", "SRS13053400", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.91468, null, 0.10225, null, 0.70688, null, 0.48401, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.205 \u00b5M Replicate 3", "GSM6165384", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.205 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165384", "GSM6165384: RNA Retene 0.205 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1208192098, 1046598883, 1088752462, 1206307357, 0, "SRX15324783", "SRS13053399", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92485, null, 0.08773, null, 0.71482, null, 0.4865, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.205 \u00b5M Replicate 2", "GSM6165383", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.205 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165383", "GSM6165383: RNA Retene 0.205 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1199051958, 1046776379, 1091726768, 1199786895, 0, "SRX15324782", "SRS13053398", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92685, null, 0.08488, null, 0.70946, null, 0.4809, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Retene 0.205 \u00b5M Replicate 1", "GSM6165382", null, "tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 \u00b5M|FISH strain:Tropical 5D", "RNA Retene 0.205 \u00b5M 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 \u00b5M", "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 \u00b5M|FISH strain:Tropical 5D", "GSM6165382", "GSM6165382: RNA Retene 0.205 \u00b5M 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1207574600, 1052993527, 1095598503, 1211009370, 0, "SRX15324781", "SRS13053397", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92733, null, 0.08445, null, 0.7083, null, 0.47655, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Vehicle control Replicate 4", "GSM6165381", null, "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 \u00b5M", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1202023760, 1052394121, 1091476117, 1208061202, 0, "SRX15324780", "SRS13053396", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92839, null, 0.0842, null, 0.70812, null, 0.48512, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Vehicle control Replicate 3", "GSM6165380", null, "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 \u00b5M", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1260496096, 1108347336, 1153576121, 1264563047, 0, "SRX15324779", "SRS13053395", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.9294, null, 0.08138, null, 0.71045, null, 0.47542, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Vehicle control Replicate 2", "GSM6165379", null, "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 \u00b5M", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1203655800, 1046900520, 1091124255, 1204988025, 0, "SRX15324778", "SRS13053394", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.92452, null, 0.09064, null, 0.69796, null, 0.46741, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, "RNA Vehicle control Replicate 1", "GSM6165378", null, "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 \u00b5M", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP375841", null, null, "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, null, null, 1200249191, 1047425766, 1091774738, 1201765705, 0, "SRX15324777", "SRS13053393", "SRA1422455", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.9255, null, 0.08609, null, 0.70816, null, 0.47434, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:38271330", null, "Foxj1b Mutant R3", "GSM7329932", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1b Control R3", "GSM7329931", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Mutant R3", "GSM7329930", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Control R3", "GSM7329929", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1b Mutant R2", "GSM7329928", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1b Control R2", "GSM7329927", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Mutant R2", "GSM7329926", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Control R2", "GSM7329925", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1b Mutant R1", "GSM7329924", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1b Control R1", "GSM7329923", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Mutant R1", "GSM7329922", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "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.", null, "pubmed:38271330", null, "Foxj1a Control R1", "GSM7329921", null, "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", null, "To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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\u2019s DNBSEQTM Technology.", "Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C 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 500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL 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\u00b0C. 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 700\u03bcL 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 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL 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 30\u03bcL 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "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, null, null, 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", null, "Unknown", "2023-05-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 57, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Multi-stage", "p1": "DNBSEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "cDNA", "label": "cDNA", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&experiment.library_selection=cDNA", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&experiment.library_selection=PolyA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "DNBSEQ", "label": "DNBSEQ", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&devstage_curation_coarse=Multi-stage", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=DNBSEQ", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&tissue_curation=Whole+Organism", "selected": false}, {"value": "Trunk", "label": "Trunk", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&tissue_curation=Trunk", "selected": false}, {"value": "Skin", "label": "Skin", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&tissue_curation=Skin", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ", "results": [{"value": "unknown", "label": "unknown", "count": 57, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Multi-stage&experiment.platform=DNBSEQ&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 118.78725199494511}