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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. 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Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1230", null, "library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 3", "H 3", "H 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz", "fastq fastq", 6117817800.0, 20392726.0, "S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz", "0:150 1:150", "A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211", 150, 150, null, null, 1635728688, 1405168032, 1464072107, 1612834762, 14211, "SRX23704452", "SRS20534448", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30659, "SRR28054754", "SRX23704451", "SRS20534446", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1229", null, "library ID:H 2|title:High 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1229 rep1 1 URNA S73 L003 R1 001.fastq|filename2:S21K1229 rep1 1 URNA S73 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 2", "H 2", "H 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1229_rep1_1_URNA_S73_L003_R1_001.fastq.gz S21K1229_rep1_1_URNA_S73_L003_R2_001.fastq.gz", "fastq fastq", 7164803100.0, 23882677.0, "S21K1229 rep1 1 URNA S73 L003 R1 001.fastq.gz", "0:150 1:150", "A:1920286881;C:1649856655;G:1697032084;T:1897610671;N:16809", 150, 150, null, null, 1920286881, 1649856655, 1697032084, 1897610671, 16809, "SRX23704451", "SRS20534446", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30660, "SRR28054755", "SRX23704450", "SRS20534445", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1220", null, "library ID:C 2|title:Control 2|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1220 rep1 1 URNA S64 L003 R1 001.fastq|filename2:S21K1220 rep1 1 URNA S64 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 2", "C 2", "C 2", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1220_rep1_1_URNA_S64_L003_R1_001.fastq.gz S21K1220_rep1_1_URNA_S64_L003_R2_001.fastq.gz", "fastq fastq", 6790504800.0, 22635016.0, "S21K1220 rep1 1 URNA S64 L003 R1 001.fastq.gz", "0:150 1:150", "A:1784553430;C:1593393319;G:1650087761;T:1762454671;N:15619", 150, 150, null, null, 1784553430, 1593393319, 1650087761, 1762454671, 15619, "SRX23704450", "SRS20534445", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30661, "SRR28054756", "SRX23704449", "SRS20534444", "SRP491086", "PRJNA1078753", "Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1219", null, "library ID:C 1|title:Control 1|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1219 rep1 1 URNA S63 L003 R1 001.fastq|filename2:S21K1219 rep1 1 URNA S63 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Control 1", "C 1", "C 1", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1219_rep1_1_URNA_S63_L003_R1_001.fastq.gz S21K1219_rep1_1_URNA_S63_L003_R2_001.fastq.gz", "fastq fastq", 7498264200.0, 24994214.0, "S21K1219 rep1 1 URNA S63 L003 R1 001.fastq.gz", "0:150 1:150", "A:2002773492;C:1716996682;G:1800329295;T:1978147319;N:17412", 150, 150, null, null, 2002773492, 1716996682, 1800329295, 1978147319, 17412, "SRX23704449", "SRS20534444", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [30691, "SRR28270998", "SRX23880961", "SRS20704477", "SRP494117", "PRJNA1085662", "Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "PRJNA1085662", "Other", "Roxithromycin ROX a commonly used macrolide antibiotic is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation ROX persists as a resilient environmental contaminant detectable in aquatic ecosystems and food products. However our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos significantly reducing hatch rates body lengths and increased malformation rates. Moreover ROX exposure adversely affected the locomotive capacity of zebrafish embryos and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons evident through reduced or irregular axonal lengths. Concurrently abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax bcl2 caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1 olig2 axon development cd82a mbpa plp1b sema5a and neuroimmunity aplnrb aplnra in zebrafish larvae. Furthermore the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.", null, null, null, null, "WT", null, "strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells", "DANIO", "DANIO", "Illumina Second Generation Sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA_oligo_dT", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP494117", null, null, "WT_S1_L001_I1_001.fastq.gz", "fastq", 7991376264.0, 998922033.0, "WT S1 L001 I1 001.fastq.gz", "0:8", "A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175", 8, null, null, null, 2573734851, 1426474966, 1492966198, 2498173074, 27175, "SRX23880961", "SRS20704477", "SRA1820072", "shantou university|Neurobiology Center", "shantou university", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 8, null, "T", null, "under 1.2% mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2024-03-11", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33254, "SRR29884387", "SRX25380731", "SRS22046084", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Male 5", "GSM8406341", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406341", "GSM8406341: Eye wh5 Male 5; Danio rerio; RNA Seq", "GSM8406341 r1", "GSM8406341", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample40KOMaleEye_R2.fastq Sample40KOMaleEye_R1.fastq", "fastq fastq", 7538485922.0, 39271929.0, "GSM8406341 r1", "0:95.98 1:95.98", "A:1967237212;C:1781996027;G:1815934363;T:1970640817;N:2677503", 95, 95, null, null, 1967237212, 1781996027, 1815934363, 1970640817, 2677503, "SRX25380731", "SRS22046084", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95183, 0.95218, 0.07853, 0.07764, 0.68146, 0.68166, 0.49087, 0.49177, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33255, "SRR29884388", "SRX25380730", "SRS22046083", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Male 4", "GSM8406340", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406340", "GSM8406340: Eye wh5 Male 4; Danio rerio; RNA Seq", "GSM8406340 r1", "GSM8406340", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample39KOMaleEye_R1.fastq Sample39KOMaleEye_R2.fastq", "fastq fastq", 7862494596.0, 40297814.0, "GSM8406340 r1", "0:97.55 1:97.55", "A:2107320803;C:1803034371;G:1842789416;T:2106566245;N:2783761", 97, 97, null, null, 2107320803, 1803034371, 1842789416, 2106566245, 2783761, "SRX25380730", "SRS22046083", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.88885, 0.89107, 0.07613, 0.07476, 0.69451, 0.69566, 0.49352, 0.50029, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33256, "SRR29884389", "SRX25380729", "SRS22046082", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Male 3", "GSM8406339", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406339", "GSM8406339: Eye wh5 Male 3; Danio rerio; RNA Seq", "GSM8406339 r1", "GSM8406339", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample38KOMaleEye_R1.fastq Sample38KOMaleEye_R2.fastq", "fastq fastq", 6479297470.0, 32901327.0, "GSM8406339 r1", "0:98.47 1:98.47", "A:1738119915;C:1487098061;G:1513025225;T:1738788853;N:2265416", 98, 98, null, null, 1738119915, 1487098061, 1513025225, 1738788853, 2265416, "SRX25380729", "SRS22046082", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94562, 0.94732, 0.07992, 0.07909, 0.69158, 0.69138, 0.50829, 0.5024, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33257, "SRR29884390", "SRX25380728", "SRS22046081", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Male 2", "GSM8406338", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406338", "GSM8406338: Eye wh5 Male 2; Danio rerio; RNA Seq", "GSM8406338 r1", "GSM8406338", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample37KOMaleEye_R1.fastq Sample37KOMaleEye_R2.fastq", "fastq fastq", 6629719076.0, 33727364.0, "GSM8406338 r1", "0:98.28 1:98.28", "A:1764705315;C:1534928212;G:1563035445;T:1764737150;N:2312954", 98, 98, null, null, 1764705315, 1534928212, 1563035445, 1764737150, 2312954, "SRX25380728", "SRS22046081", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95253, 0.95618, 0.07586, 0.07516, 0.69282, 0.69221, 0.49593, 0.4823, 69, 69, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33258, "SRR29884391", "SRX25380727", "SRS22046080", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Male 1", "GSM8406337", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406337", "GSM8406337: Eye wh5 Male 1; Danio rerio; RNA Seq", "GSM8406337 r1", "GSM8406337", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample36KOMaleEye_R1.fastq Sample36KOMaleEye_R2.fastq", "fastq fastq", 5709061918.0, 28979886.0, "GSM8406337 r1", "0:98.50 1:98.50", "A:1522981393;C:1321621825;G:1340646747;T:1521818110;N:1993843", 98, 98, null, null, 1522981393, 1321621825, 1340646747, 1521818110, 1993843, "SRX25380727", "SRS22046080", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94615, 0.94747, 0.11492, 0.11272, 0.68436, 0.68446, 0.51813, 0.5179, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33259, "SRR29884392", "SRX25380726", "SRS22046079", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Female 5", "GSM8406336", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406336", "GSM8406336: Eye wh5 Female 5; Danio rerio; RNA Seq", "GSM8406336 r1", "GSM8406336", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample35KOFemaleEye_R1.fastq Sample35KOFemaleEye_R2.fastq", "fastq fastq", 5427070458.0, 28381536.0, "GSM8406336 r1", "0:95.61 1:95.61", "A:1415064176;C:1287586920;G:1304802479;T:1417689072;N:1927811", 95, 95, null, null, 1415064176, 1287586920, 1304802479, 1417689072, 1927811, "SRX25380726", "SRS22046079", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94227, 0.94361, 0.11567, 0.11449, 0.67452, 0.67442, 0.49494, 0.49637, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33260, "SRR29884393", "SRX25380725", "SRS22046078", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Female 4", "GSM8406335", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406335", "GSM8406335: Eye wh5 Female 4; Danio rerio; RNA Seq", "GSM8406335 r1", "GSM8406335", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample34KOFemaleEye_R1.fastq Sample34KOFemaleEye_R2.fastq", "fastq fastq", 7147923902.0, 36321130.0, "GSM8406335 r1", "0:98.40 1:98.40", "A:1915214130;C:1645720125;G:1671289633;T:1913205077;N:2494937", 98, 98, null, null, 1915214130, 1645720125, 1671289633, 1913205077, 2494937, "SRX25380725", "SRS22046078", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94673, 0.9495, 0.10846, 0.10716, 0.68546, 0.68576, 0.50162, 0.51282, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33261, "SRR29884394", "SRX25380724", "SRS22046077", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Female 3", "GSM8406334", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406334", "GSM8406334: Eye wh5 Female 3; Danio rerio; RNA Seq", "GSM8406334 r1", "GSM8406334", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample33KOFemaleEye_R1.fastq Sample33KOFemaleEye_R2.fastq", "fastq fastq", 5282619330.0, 26862421.0, "GSM8406334 r1", "0:98.33 1:98.33", "A:1401322632;C:1228726745;G:1250721810;T:1400000047;N:1848096", 98, 98, null, null, 1401322632, 1228726745, 1250721810, 1400000047, 1848096, "SRX25380724", "SRS22046077", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94918, 0.95136, 0.09986, 0.09846, 0.68406, 0.68343, 0.50791, 0.50912, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33262, "SRR29884395", "SRX25380723", "SRS22046076", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Female 2", "GSM8406333", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406333", "GSM8406333: Eye wh5 Female 2; Danio rerio; RNA Seq", "GSM8406333 r1", "GSM8406333", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample32KOFemaleEye_R1.fastq Sample32KOFemaleEye_R2.fastq", "fastq fastq", 5138054606.0, 26117176.0, "GSM8406333 r1", "0:98.37 1:98.37", "A:1362190516;C:1195339408;G:1217795589;T:1360934102;N:1794991", 98, 98, null, null, 1362190516, 1195339408, 1217795589, 1360934102, 1794991, "SRX25380723", "SRS22046076", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.95053, 0.95112, 0.11959, 0.11702, 0.68564, 0.68487, 0.53365, 0.52549, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33263, "SRR29884396", "SRX25380722", "SRS22046075", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye wh5 Female 1", "GSM8406332", null, "source name:brain|tissue:brain|genotype:wh5|geo loc name:missing|collection date:missing", "Eye wh5 Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:wh5", "GSM8406332", "GSM8406332: Eye wh5 Female 1; Danio rerio; RNA Seq", "GSM8406332 r1", "GSM8406332", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample31KOFemaleEye_R1.fastq Sample31KOFemaleEye_R2.fastq", "fastq fastq", 10220677680.0, 51930769.0, "GSM8406332 r1", "0:98.41 1:98.41", "A:2678910180;C:2403108978;G:2460841265;T:2674251113;N:3566144", 98, 98, null, null, 2678910180, 2403108978, 2460841265, 2674251113, 3566144, "SRX25380722", "SRS22046075", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94832, 0.95149, 0.11677, 0.11536, 0.69199, 0.69144, 0.51108, 0.51355, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33264, "SRR29884397", "SRX25380721", "SRS22046073", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Male 5", "GSM8406331", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406331", "GSM8406331: Eye WT Male 5; Danio rerio; RNA Seq", "GSM8406331 r1", "GSM8406331", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample30WTMaleEye_R1.fastq Sample30WTMaleEye_R2.fastq", "fastq fastq", 6485687400.0, 33002416.0, "GSM8406331 r1", "0:98.26 1:98.26", "A:1728466253;C:1500931006;G:1524828714;T:1729195053;N:2266374", 98, 98, null, null, 1728466253, 1500931006, 1524828714, 1729195053, 2266374, "SRX25380721", "SRS22046073", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94722, 0.94937, 0.10433, 0.10291, 0.68883, 0.68939, 0.49445, 0.46638, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33265, "SRR29884398", "SRX25380720", "SRS22046074", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Male 4", "GSM8406330", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406330", "GSM8406330: Eye WT Male 4; Danio rerio; RNA Seq", "GSM8406330 r1", "GSM8406330", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample29WTMaleEye_R1.fastq Sample29WTMaleEye_R2.fastq", "fastq fastq", 7062083656.0, 35791158.0, "GSM8406330 r1", "0:98.66 1:98.66", "A:1894520544;C:1621849694;G:1646676208;T:1896586465;N:2450745", 98, 98, null, null, 1894520544, 1621849694, 1646676208, 1896586465, 2450745, "SRX25380720", "SRS22046074", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9467, 0.94857, 0.11004, 0.1075, 0.68657, 0.686, 0.50982, 0.50696, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33266, "SRR29884399", "SRX25380719", "SRS22046072", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Male 3", "GSM8406329", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406329", "GSM8406329: Eye WT Male 3; Danio rerio; RNA Seq", "GSM8406329 r1", "GSM8406329", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample28WTMaleEye_R2.fastq Sample28WTMaleEye_R1.fastq", "fastq fastq", 6460573656.0, 32912157.0, "GSM8406329 r1", "0:98.15 1:98.15", "A:1734329877;C:1484525299;G:1504584680;T:1734881748;N:2252052", 98, 98, null, null, 1734329877, 1484525299, 1504584680, 1734881748, 2252052, "SRX25380719", "SRS22046072", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94094, 0.94266, 0.11467, 0.113, 0.68574, 0.68511, 0.52613, 0.49429, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33267, "SRR29884400", "SRX25380718", "SRS22046071", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Male 2", "GSM8406328", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406328", "GSM8406328: Eye WT Male 2; Danio rerio; RNA Seq", "GSM8406328 r1", "GSM8406328", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample27WTMaleEye_R1.fastq Sample27WTMaleEye_R2.fastq", "fastq fastq", 8379349662.0, 42809191.0, "GSM8406328 r1", "0:97.87 1:97.87", "A:2236044006;C:1937171487;G:1969824761;T:2233423000;N:2886408", 97, 97, null, null, 2236044006, 1937171487, 1969824761, 2233423000, 2886408, "SRX25380718", "SRS22046071", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94985, 0.95265, 0.0973, 0.09565, 0.68814, 0.68868, 0.49928, 0.50187, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33268, "SRR29884401", "SRX25380717", "SRS22046070", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Male 1", "GSM8406327", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406327", "GSM8406327: Eye WT Male 1; Danio rerio; RNA Seq", "GSM8406327 r1", "GSM8406327", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample26WTMaleEye_R1.fastq Sample26WTMaleEye_R2.fastq", "fastq fastq", 6903877724.0, 35162472.0, "GSM8406327 r1", "0:98.17 1:98.17", "A:1834111504;C:1600540211;G:1632902994;T:1833911892;N:2411123", 98, 98, null, null, 1834111504, 1600540211, 1632902994, 1833911892, 2411123, "SRX25380717", "SRS22046070", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94845, 0.94881, 0.10868, 0.106, 0.68684, 0.68647, 0.51253, 0.51184, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33269, "SRR29884402", "SRX25380716", "SRS22046069", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Female 5", "GSM8406326", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406326", "GSM8406326: Eye WT Female 5; Danio rerio; RNA Seq", "GSM8406326 r1", "GSM8406326", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample25WTFemaleEye_R1.fastq Sample25WTFemaleEye_R2.fastq", "fastq fastq", 6008109144.0, 30559574.0, "GSM8406326 r1", "0:98.30 1:98.30", "A:1602153382;C:1384849253;G:1417624141;T:1601373961;N:2108407", 98, 98, null, null, 1602153382, 1384849253, 1417624141, 1601373961, 2108407, "SRX25380716", "SRS22046069", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94455, 0.94527, 0.11551, 0.11357, 0.68294, 0.68337, 0.52076, 0.51087, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33270, "SRR29884403", "SRX25380715", "SRS22046068", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Female 4", "GSM8406325", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406325", "GSM8406325: Eye WT Female 4; Danio rerio; RNA Seq", "GSM8406325 r1", "GSM8406325", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample24WTFemaleEye_R1.fastq Sample24WTFemaleEye_R2.fastq", "fastq fastq", 7279680362.0, 36932422.0, "GSM8406325 r1", "0:98.55 1:98.55", "A:1970880191;C:1653556002;G:1681116124;T:1971590390;N:2537655", 98, 98, null, null, 1970880191, 1653556002, 1681116124, 1971590390, 2537655, "SRX25380715", "SRS22046068", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94446, 0.945, 0.11353, 0.11157, 0.69053, 0.69002, 0.51519, 0.51315, 90, 90, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33271, "SRR29884404", "SRX25380714", "SRS22046067", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Female 3", "GSM8406324", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406324", "GSM8406324: Eye WT Female 3; Danio rerio; RNA Seq", "GSM8406324 r1", "GSM8406324", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample23WTFemaleEye_R1.fastq Sample23WTFemaleEye_R2.fastq", "fastq fastq", 5569794970.0, 28366560.0, "GSM8406324 r1", "0:98.18 1:98.18", "A:1484725199;C:1288582787;G:1309580985;T:1484962225;N:1943774", 98, 98, null, null, 1484725199, 1288582787, 1309580985, 1484962225, 1943774, "SRX25380714", "SRS22046067", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94662, 0.94876, 0.11169, 0.10977, 0.68783, 0.68738, 0.49232, 0.49903, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33272, "SRR29884405", "SRX25380713", "SRS22046065", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Female 2", "GSM8406323", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406323", "GSM8406323: Eye WT Female 2; Danio rerio; RNA Seq", "GSM8406323 r1", "GSM8406323", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample22WTFemaleEye_R1.fastq Sample22WTFemaleEye_R2.fastq", "fastq fastq", 5686067464.0, 28940004.0, "GSM8406323 r1", "0:98.24 1:98.24", "A:1516704497;C:1314340450;G:1336741473;T:1516301403;N:1979641", 98, 98, null, null, 1516704497, 1314340450, 1336741473, 1516301403, 1979641, "SRX25380713", "SRS22046065", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94887, 0.94762, 0.11186, 0.10985, 0.68426, 0.68357, 0.50264, 0.51594, 92, 92, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33273, "SRR29884406", "SRX25380712", "SRS22046066", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Eye WT Female 1", "GSM8406322", null, "source name:brain|tissue:brain|genotype:WT|geo loc name:missing|collection date:missing", "Eye WT Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "brain", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:brain|genotype:WT", "GSM8406322", "GSM8406322: Eye WT Female 1; Danio rerio; RNA Seq", "GSM8406322 r1", "GSM8406322", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample21WTFemaleEye_R1.fastq Sample21WTFemaleEye_R2.fastq", "fastq fastq", 6263798100.0, 31891210.0, "GSM8406322 r1", "0:98.21 1:98.21", "A:1677507851;C:1442844053;G:1464527035;T:1676734488;N:2184673", 98, 98, null, null, 1677507851, 1442844053, 1464527035, 1676734488, 2184673, "SRX25380712", "SRS22046066", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.949, 0.95043, 0.10639, 0.10415, 0.69165, 0.69027, 0.51009, 0.51397, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [33274, "SRR29884407", "SRX25380711", "SRS22046064", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 5", "GSM8406321", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406321", "GSM8406321: Brain wh5 Male 5; Danio rerio; RNA Seq", "GSM8406321 r1", "GSM8406321", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample20KOMaleBrain_R1.fastq Sample20KOMaleBrain_R2.fastq", "fastq fastq", 5509276088.0, 27917150.0, "GSM8406321 r1", "0:98.67 1:98.67", "A:1498190193;C:1242495192;G:1267229536;T:1499431726;N:1929441", 98, 98, null, null, 1498190193, 1242495192, 1267229536, 1499431726, 1929441, "SRX25380711", "SRS22046064", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94576, 0.94515, 0.14102, 0.13871, 0.69187, 0.69077, 0.52554, 0.53007, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33275, "SRR29884408", "SRX25380710", "SRS22046063", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 4", "GSM8406320", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406320", "GSM8406320: Brain wh5 Male 4; Danio rerio; RNA Seq", "GSM8406320 r1", "GSM8406320", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample19KOMaleBrain_R1.fastq Sample19KOMaleBrain_R2.fastq", "fastq fastq", 6985356408.0, 35379007.0, "GSM8406320 r1", "0:98.72 1:98.72", "A:1889039547;C:1582622229;G:1620512342;T:1890746302;N:2435988", 98, 98, null, null, 1889039547, 1582622229, 1620512342, 1890746302, 2435988, "SRX25380710", "SRS22046063", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94197, 0.94411, 0.14763, 0.14597, 0.69852, 0.69826, 0.54705, 0.54822, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33276, "SRR29884409", "SRX25380709", "SRS22046062", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 3", "GSM8406319", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406319", "GSM8406319: Brain wh5 Male 3; Danio rerio; RNA Seq", "GSM8406319 r1", "GSM8406319", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample18KOMaleBrain_R1.fastq Sample18KOMaleBrain_R2.fastq", "fastq fastq", 5864072768.0, 29837549.0, "GSM8406319 r1", "0:98.27 1:98.27", "A:1609423180;C:1310248473;G:1328624911;T:1613750029;N:2026175", 98, 98, null, null, 1609423180, 1310248473, 1328624911, 1613750029, 2026175, "SRX25380709", "SRS22046062", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94007, 0.94233, 0.14021, 0.1386, 0.69376, 0.69317, 0.51507, 0.52214, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33277, "SRR29884410", "SRX25380708", "SRS22046061", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 2", "GSM8406318", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406318", "GSM8406318: Brain wh5 Male 2; Danio rerio; RNA Seq", "GSM8406318 r1", "GSM8406318", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample17KOMaleBrain_R1.fastq Sample17KOMaleBrain_R2.fastq", "fastq fastq", 5841328432.0, 29860768.0, "GSM8406318 r1", "0:97.81 1:97.81", "A:1606036785;C:1302920703;G:1321021765;T:1609306125;N:2043054", 97, 97, null, null, 1606036785, 1302920703, 1321021765, 1609306125, 2043054, "SRX25380708", "SRS22046061", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9429, 0.94295, 0.14247, 0.14023, 0.69808, 0.69739, 0.51804, 0.51798, 69, 69, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33278, "SRR29884411", "SRX25380707", "SRS22046060", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Male 1", "GSM8406317", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406317", "GSM8406317: Brain wh5 Male 1; Danio rerio; RNA Seq", "GSM8406317 r1", "GSM8406317", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample16KOMaleBrain_R1.fastq Sample16KOMaleBrain_R2.fastq", "fastq fastq", 6061816166.0, 30929476.0, "GSM8406317 r1", "0:97.99 1:97.99", "A:1666435568;C:1352308656;G:1373281492;T:1667671946;N:2118504", 97, 97, null, null, 1666435568, 1352308656, 1373281492, 1667671946, 2118504, "SRX25380707", "SRS22046060", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94198, 0.9434, 0.14745, 0.14621, 0.69201, 0.69138, 0.52388, 0.52247, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33279, "SRR29884412", "SRX25380706", "SRS22046059", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 5", "GSM8406316", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406316", "GSM8406316: Brain wh5 Female 5; Danio rerio; RNA Seq", "GSM8406316 r1", "GSM8406316", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample15KOFemaleBrain_R1.fastq Sample15KOFemaleBrain_R2.fastq", "fastq fastq", 5830172008.0, 29715950.0, "GSM8406316 r1", "0:98.10 1:98.10", "A:1585225847;C:1316585087;G:1339955604;T:1586384657;N:2020813", 98, 98, null, null, 1585225847, 1316585087, 1339955604, 1586384657, 2020813, "SRX25380706", "SRS22046059", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94307, 0.94571, 0.13598, 0.13423, 0.69341, 0.69309, 0.52103, 0.50706, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33280, "SRR29884413", "SRX25380705", "SRS22046058", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 4", "GSM8406315", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406315", "GSM8406315: Brain wh5 Female 4; Danio rerio; RNA Seq", "GSM8406315 r1", "GSM8406315", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample14KOFemaleBrain_R1.fastq Sample14KOFemaleBrain_R2.fastq", "fastq fastq", 6700791892.0, 34096304.0, "GSM8406315 r1", "0:98.26 1:98.26", "A:1817874372;C:1516000049;G:1546573687;T:1818017657;N:2326127", 98, 98, null, null, 1817874372, 1516000049, 1546573687, 1818017657, 2326127, "SRX25380705", "SRS22046058", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94342, 0.94623, 0.13719, 0.13523, 0.69313, 0.69254, 0.53293, 0.53816, 84, 84, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33281, "SRR29884414", "SRX25380704", "SRS22046057", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 3", "GSM8406314", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406314", "GSM8406314: Brain wh5 Female 3; Danio rerio; RNA Seq", "GSM8406314 r1", "GSM8406314", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample13KOFemaleBrain_R2.fastq Sample13KOFemaleBrain_R1.fastq", "fastq fastq", 6308152444.0, 32040291.0, "GSM8406314 r1", "0:98.44 1:98.44", "A:1698706705;C:1436132175;G:1472501608;T:1698611730;N:2200226", 98, 98, null, null, 1698706705, 1436132175, 1472501608, 1698611730, 2200226, "SRX25380704", "SRS22046057", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94654, 0.94476, 0.1362, 0.13304, 0.694, 0.69321, 0.54515, 0.53479, 91, 91, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33282, "SRR29884415", "SRX25380703", "SRS22046056", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 2", "GSM8406313", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406313", "GSM8406313: Brain wh5 Female 2; Danio rerio; RNA Seq", "GSM8406313 r1", "GSM8406313", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample12KOFemaleBrain_R1.fastq Sample12KOFemaleBrain_R2.fastq", "fastq fastq", 6503673262.0, 33197897.0, "GSM8406313 r1", "0:97.95 1:97.95", "A:1781196226;C:1457467194;G:1479672271;T:1783090598;N:2246973", 97, 97, null, null, 1781196226, 1457467194, 1479672271, 1783090598, 2246973, "SRX25380703", "SRS22046056", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94227, 0.94462, 0.13793, 0.13614, 0.69359, 0.69355, 0.52971, 0.52982, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33283, "SRR29884416", "SRX25380702", "SRS22046055", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain wh5 Female 1", "GSM8406312", null, "source name:eye|tissue:eye|genotype:wh5|geo loc name:missing|collection date:missing", "Brain wh5 Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:wh5", "GSM8406312", "GSM8406312: Brain wh5 Female 1; Danio rerio; RNA Seq", "GSM8406312 r1", "GSM8406312", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample11KOFemaleBrain_R1.fastq Sample11KOFemaleBrain_R2.fastq", "fastq fastq", 5803578222.0, 29408217.0, "GSM8406312 r1", "0:98.67 1:98.67", "A:1586553028;C:1303184285;G:1323602566;T:1588219875;N:2018468", 98, 98, null, null, 1586553028, 1303184285, 1323602566, 1588219875, 2018468, "SRX25380702", "SRS22046055", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94183, 0.94513, 0.1442, 0.14286, 0.6942, 0.6942, 0.51627, 0.51673, 93, 93, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33284, "SRR29884417", "SRX25380701", "SRS22046053", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 5", "GSM8406311", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406311", "GSM8406311: Brain WT Male 5; Danio rerio; RNA Seq", "GSM8406311 r1", "GSM8406311", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample10WTMaleBrain_R1.fastq Sample10WTMaleBrain_R2.fastq", "fastq fastq", 4558024898.0, 24051338.0, "GSM8406311 r1", "0:94.76 1:94.76", "A:1220269093;C:1048518583;G:1068311203;T:1219299559;N:1626460", 94, 94, null, null, 1220269093, 1048518583, 1068311203, 1219299559, 1626460, "SRX25380701", "SRS22046053", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.93188, 0.93167, 0.1413, 0.13958, 0.70814, 0.70875, 0.52962, 0.53051, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33285, "SRR29884418", "SRX25380700", "SRS22046052", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 4", "GSM8406310", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406310", "GSM8406310: Brain WT Male 4; Danio rerio; RNA Seq", "GSM8406310 r1", "GSM8406310", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample9WTMaleBrain_R1.fastq Sample9WTMaleBrain_R2.fastq", "fastq fastq", 5130577372.0, 26157026.0, "GSM8406310 r1", "0:98.07 1:98.07", "A:1409899035;C:1143333235;G:1163465644;T:1412102322;N:1777136", 98, 98, null, null, 1409899035, 1143333235, 1163465644, 1412102322, 1777136, "SRX25380700", "SRS22046052", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94388, 0.94533, 0.13794, 0.13603, 0.69907, 0.69867, 0.52585, 0.51928, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33286, "SRR29884419", "SRX25380699", "SRS22046054", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 3", "GSM8406309", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406309", "GSM8406309: Brain WT Male 3; Danio rerio; RNA Seq", "GSM8406309 r1", "GSM8406309", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample8WTMaleBrain_R1.fastq Sample8WTMaleBrain_R2.fastq", "fastq fastq", 7972815402.0, 40447690.0, "GSM8406309 r1", "0:98.56 1:98.56", "A:2168632819;C:1797135023;G:1834247957;T:2170022014;N:2777589", 98, 98, null, null, 2168632819, 1797135023, 1834247957, 2170022014, 2777589, "SRX25380699", "SRS22046054", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94357, 0.94705, 0.13542, 0.13436, 0.69915, 0.69863, 0.52491, 0.53063, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33287, "SRR29884420", "SRX25380698", "SRS22046051", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 2", "GSM8406308", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406308", "GSM8406308: Brain WT Male 2; Danio rerio; RNA Seq", "GSM8406308 r1", "GSM8406308", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample7WTMaleBrain_R1.fastq Sample7WTMaleBrain_R2.fastq", "fastq fastq", 7049713238.0, 35734267.0, "GSM8406308 r1", "0:98.64 1:98.64", "A:1906626428;C:1601451933;G:1627879106;T:1911302856;N:2452915", 98, 98, null, null, 1906626428, 1601451933, 1627879106, 1911302856, 2452915, "SRX25380698", "SRS22046051", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.9436, 0.94611, 0.15189, 0.14982, 0.70272, 0.70293, 0.54976, 0.55028, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33288, "SRR29884421", "SRX25380697", "SRS22046050", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Male 1", "GSM8406307", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Male 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406307", "GSM8406307: Brain WT Male 1; Danio rerio; RNA Seq", "GSM8406307 r1", "GSM8406307", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample6WTMaleBrain_R1.fastq Sample6WTMaleBrain_R2.fastq", "fastq fastq", 5957369076.0, 30406342.0, "GSM8406307 r1", "0:97.96 1:97.96", "A:1609314070;C:1357455510;G:1376051649;T:1612447643;N:2100204", 97, 97, null, null, 1609314070, 1357455510, 1376051649, 1612447643, 2100204, "SRX25380697", "SRS22046050", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94515, 0.94596, 0.13859, 0.13741, 0.69459, 0.69386, 0.5113, 0.50829, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33289, "SRR29884422", "SRX25380696", "SRS22046048", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 5", "GSM8406306", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 5", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406306", "GSM8406306: Brain WT Female 5; Danio rerio; RNA Seq", "GSM8406306 r1", "GSM8406306", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample5WTFemaleBrain_R1.fastq Sample5WTFemaleBrain_R2.fastq", "fastq fastq", 6253800764.0, 31754862.0, "GSM8406306 r1", "0:98.47 1:98.47", "A:1706349321;C:1408396210;G:1425535859;T:1711348232;N:2171142", 98, 98, null, null, 1706349321, 1408396210, 1425535859, 1711348232, 2171142, "SRX25380696", "SRS22046048", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94054, 0.9433, 0.13645, 0.13468, 0.69351, 0.69268, 0.50849, 0.50886, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33290, "SRR29884423", "SRX25380695", "SRS22046047", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 4", "GSM8406305", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 4", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406305", "GSM8406305: Brain WT Female 4; Danio rerio; RNA Seq", "GSM8406305 r1", "GSM8406305", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample4WTFemaleBrain_R1.fastq Sample4WTFemaleBrain_R2.fastq", "fastq fastq", 6326747176.0, 32181924.0, "GSM8406305 r1", "0:98.30 1:98.30", "A:1726705163;C:1423533467;G:1441282364;T:1733022638;N:2203544", 98, 98, null, null, 1726705163, 1423533467, 1441282364, 1733022638, 2203544, "SRX25380695", "SRS22046047", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94564, 0.9463, 0.13279, 0.13015, 0.69329, 0.69264, 0.52131, 0.52995, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33291, "SRR29884424", "SRX25380694", "SRS22046049", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 3", "GSM8406304", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 3", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406304", "GSM8406304: Brain WT Female 3; Danio rerio; RNA Seq", "GSM8406304 r1", "GSM8406304", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample3WTFemaleBrain_R1.fastq Sample3WTFemaleBrain_R2.fastq", "fastq fastq", 6158432042.0, 31268580.0, "GSM8406304 r1", "0:98.48 1:98.48", "A:1663143400;C:1401049481;G:1427904493;T:1664192587;N:2142081", 98, 98, null, null, 1663143400, 1401049481, 1427904493, 1664192587, 2142081, "SRX25380694", "SRS22046049", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94243, 0.94497, 0.13191, 0.13006, 0.68454, 0.68335, 0.53268, 0.53362, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33292, "SRR29884425", "SRX25380693", "SRS22046046", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 2", "GSM8406303", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 2", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406303", "GSM8406303: Brain WT Female 2; Danio rerio; RNA Seq", "GSM8406303 r1", "GSM8406303", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP520852", null, null, "Sample2WTFemaleBrain_R1.fastq Sample2WTFemaleBrain_R2.fastq", "fastq fastq", 5029227086.0, 25468404.0, "GSM8406303 r1", "0:98.73 1:98.73", "A:1373457097;C:1129749557;G:1148614258;T:1375648797;N:1757377", 98, 98, null, null, 1373457097, 1129749557, 1148614258, 1375648797, 1757377, "SRX25380693", "SRS22046046", "SRA1927371", "Oregon State University", "Oregon State University", 2, 0.94244, 0.94484, 0.14143, 0.13943, 0.69414, 0.69292, 0.52985, 0.53107, 101, 101, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-07-18", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [33293, "SRR29884426", "SRX25380692", "SRS22046045", "SRP520852", "PRJNA1137393", "Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles affecting ocular and neurobehavioral function", "GSE272589", "Transcriptome Analysis", "Cytochrome P450 1B1 CYP1B1 is an enzyme that metabolizes endogenous and xenobiotic compounds. CYP1B1 is thought to be involved in the metabolism of compounds vital to the proper development of the eye. Studies have identified CYP1B1 as a causative gene in the ocular disease primary congenital glaucoma PCG however CYP1B1's role in PCG development and related eye disorders is poorly understood. To explore CYP1B1's role an in vivo zebrafish Danio rerio model was used. This study sought to determine if knocking out CYP1B1 produced an ocular defect similar to PCG and whether this could be distinguished from other neurobehavioral effects. To do this a new CYP1B1 knockout line wh5 was generated using CRISPR/Cas9 induced deletions truncating the protein before the catalytic domain. Behavior assays untargeted metabolomics and RNA sequencing was used to determine the phenotype of the wh5 line. RNA sequencing based transcriptomics was performed on adult eye and brain samples. 95 genes in the eye and 45 genes in the brain were found to be differentially expressed between the genotypes. Untargeted metabolomics analysis was performed on the same tissue type and pathway analysis was performed on the separate data sets. KEGG pathways involved in lipid steroid amino acid and nitrogen metabolism were found to be significantly perturbed. A joint pathway multi omics analysis was performed introducing gene interactions into the metabolomics pathway analysis. wh5 zebrafish performed significantly different in multiple larval and adult behavior assays however an ocular defect could not be distinguished from other neurobehavioral phenotypes due to large metabolic and transcriptomic changes in both organs. Overall design: To investigate the role of CYP1B1 in the eye and and brain a CYP1B1 knockout zebrafish line wh5 was used. Adult zebrafish whole eyes and brains were dissected. Five replicates of each sample type were sequenced: sex genotype WT or KO wh5 and organ for a total of 40 samples.", null, "pubmed:39890032", null, "Brain WT Female 1", "GSM8406302", null, "source name:eye|tissue:eye|genotype:WT|geo loc name:missing|collection date:missing", "Brain WT Female 1", "quality trimmimg and adapter removal was performed using fastp with defualt settings reads were mapped to the GRCz11 primary assembly using the STAR aligner The Lawson Lab published a zebrafish annotation Lawson et al. 2020. Both the genome assembly file and the annotation gtf file v. 4.3.2 were downloaded from their website https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome. The arguments used in the mapping step included alignIntronMin 15 alignIntronMax 250000 and quantMode GeneCounts DESeq2 v. 1.32.0 was used to explore the overall clustering of the brain and eye samples DESeq2 v. 1.32.0 was used to explore clustering of the brain and eye samples. The design formula for the DESeqDataSet object was design = Sex + Group where the groups included brain KO wh5 brain WT eye KO wh5 and eye WT. Genes with a count < 10 were removed. The filtered gene matrix included 30 921 genes. Variance stabilizing transformation blind = FALSE was applied to the data and used for the generation of the PCA including all filtered genes MDS and heatmap plots. Sample10 brain WT male was an outlier in all three plots. In addition Sample3 brain WT female appeared to be an outlier on the heatmap. From PCA and MDS plots generated separately for the brain and eye samples it could be seen that both samples appeared to be outliers on the brain sample plots. Further DEG analysis was performed using the NetworkAnalyst v3.0 web interface Of the 36 351 features in the table 25 411 69% could be matched to gene level Entrez expression and low abundance features counts < 4 and low variance feature variance percentile rank < 15 were removed DESeq2 was selected as the statistical method with wh5 vs WT comparisons being made. Features with an adjusted p value \u2264 0.05 and log2fold change \u2265 |1| were considered DEGs Assembly: GRCz11 Supplementary files format and content: .xlsx raw counts of all samples and types Supplementary files format and content: .csv separate DEG analysis results table for eye and brain with sample 3 and 10 removed", "eye", null, "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. Library preparation was performed using the NEBNext UltraExpress RNA Library Prep Kit for Illumina with a PolyA mRNA isolation kit", null, "tissue:eye|genotype:WT", "GSM8406302", "GSM8406302: Brain WT Female 1; Danio rerio; RNA Seq", "GSM8406302 r1", "GSM8406302", "1", "RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50\u00b5L of UP water and RNA quantity and quality measurements were taken using an Agilent 4150 TapeStation System. 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Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "A 3.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "A 3.0.2", "A 3.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz", "fastq fastq", 2072387100.0, 20723871.0, "HI.4079.001.Index 4.A R1.fastq.gz", "0:100 1:0", "A:539231555;C:478779687;G:466992364;T:587014266;N:369228", 100, 0, null, null, 539231555, 478779687, 466992364, 587014266, 369228, "SRX2768777", "SRS2152486", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94094, null, 0.13282, null, 0.67566, null, 0.46135, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42198, "SRR5485640", "SRX2768776", "SRS2152485", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "B 3.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "B 3.5.2", "B 3.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz", "fastq fastq", 2236492200.0, 22364922.0, "HI.4079.001.Index 5.B R1.fastq.gz", "0:100 1:0", "A:580646206;C:518191209;G:502712894;T:634542622;N:399269", 100, 0, null, null, 580646206, 518191209, 502712894, 634542622, 399269, "SRX2768776", "SRS2152485", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94188, null, 0.13073, null, 0.67653, null, 0.4635, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42199, "SRR5485639", "SRX2768775", "SRS2152484", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "C 3.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "C 3.20.2", "C 3.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz", "fastq fastq", 1979628000.0, 19796280.0, "HI.4079.001.Index 12.C R1.fastq.gz", "0:100 1:0", "A:519406228;C:453563284;G:442115002;T:564195493;N:347993", 100, 0, null, null, 519406228, 453563284, 442115002, 564195493, 347993, "SRX2768775", "SRS2152484", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93946, null, 0.14364, null, 0.6759, null, 0.46247, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42200, "SRR5485638", "SRX2768774", "SRS2152483", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "D 3.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "D 3.0.14", "D 3.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz", "fastq fastq", 1856095600.0, 18560956.0, "HI.4079.001.Index 19.D R1.fastq.gz", "0:100 1:0", "A:492424946;C:416504198;G:409645413;T:537196088;N:324955", 100, 0, null, null, 492424946, 416504198, 409645413, 537196088, 324955, "SRX2768774", "SRS2152483", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.9288, null, 0.15497, null, 0.69232, null, 0.46842, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42201, "SRR5485637", "SRX2768773", "SRS2152481", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "E 3.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "E 3.5.14", "E 3.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz", "fastq fastq", 2936761500.0, 29367615.0, "HI.4079.001.Index 1.E R1.fastq.gz", "0:100 1:0", "A:762661816;C:675701333;G:661832769;T:836033713;N:531869", 100, 0, null, null, 762661816, 675701333, 661832769, 836033713, 531869, "SRX2768773", "SRS2152481", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93957, null, 0.12499, null, 0.67714, null, 0.4697, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2017-05-08", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42202, "SRR5485636", "SRX2768772", "SRS2152480", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "F 3.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "F 3.20.14", "F 3.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz", "fastq fastq", 2169884500.0, 21698845.0, "HI.4079.001.Index 3.F R1.fastq.gz", "0:100 1:0", "A:566808272;C:496620769;G:487930959;T:618144722;N:379778", 100, 0, null, null, 566808272, 496620769, 487930959, 618144722, 379778, "SRX2768772", "SRS2152480", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93678, null, 0.13131, null, 0.67635, null, 0.47972, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42203, "SRR5485635", "SRX2768771", "SRS2152482", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "G 4.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "G 4.0.2", "G 4.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz", "fastq fastq", 2008051800.0, 20080518.0, "HI.4079.001.Index 9.G R1.fastq.gz", "0:100 1:0", "A:518304309;C:466602325;G:455957803;T:566834696;N:352667", 100, 0, null, null, 518304309, 466602325, 455957803, 566834696, 352667, "SRX2768771", "SRS2152482", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94445, null, 0.12419, null, 0.68201, null, 0.46743, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42204, "SRR5485634", "SRX2768770", "SRS2152479", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "H 4.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "H 4.5.2", "H 4.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz", "fastq fastq", 1908097900.0, 19080979.0, "HI.4079.001.Index 8.H R1.fastq.gz", "0:100 1:0", "A:494318032;C:441931870;G:431477592;T:540030651;N:339755", 100, 0, null, null, 494318032, 441931870, 431477592, 540030651, 339755, "SRX2768770", "SRS2152479", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94216, null, 0.1306, null, 0.68195, null, 0.45834, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42205, "SRR5485633", "SRX2768769", "SRS2152477", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "I 4.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "I 4.20.2", "I 4.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz", "fastq fastq", 2059931100.0, 20599311.0, "HI.4079.001.Index 10.I R1.fastq.gz", "0:100 1:0", "A:536731862;C:475769707;G:462890515;T:584183211;N:355805", 100, 0, null, null, 536731862, 475769707, 462890515, 584183211, 355805, "SRX2768769", "SRS2152477", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93561, null, 0.13393, null, 0.68225, null, 0.46489, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42206, "SRR5485632", "SRX2768768", "SRS2152478", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "J 4.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "J 4.0.14", "J 4.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz", "fastq fastq", 2199504800.0, 21995048.0, "HI.4079.001.Index 11.J R1.fastq.gz", "0:100 1:0", "A:579625731;C:499663817;G:489173373;T:630657278;N:384601", 100, 0, null, null, 579625731, 499663817, 489173373, 630657278, 384601, "SRX2768768", "SRS2152478", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93523, null, 0.13836, null, 0.68655, null, 0.47839, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42207, "SRR5485631", "SRX2768767", "SRS2152475", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "K 4.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "K 4.5.14", "K 4.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz", "fastq fastq", 2154282200.0, 21542822.0, "HI.4079.001.Index 20.K R1.fastq.gz", "0:100 1:0", "A:563358732;C:494058898;G:482596638;T:613890813;N:377119", 100, 0, null, null, 563358732, 494058898, 482596638, 613890813, 377119, "SRX2768767", "SRS2152475", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93863, null, 0.12932, null, 0.67801, null, 0.46426, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42208, "SRR5485630", "SRX2768766", "SRS2152476", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. 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The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "M 5.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "M 5.0.2", "M 5.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz", "fastq fastq", 1999183400.0, 19991834.0, "HI.4079.001.Index 25.M R1.fastq.gz", "0:100 1:0", "A:526344986;C:456726468;G:447467581;T:568292150;N:352215", 100, 0, null, null, 526344986, 456726468, 447467581, 568292150, 352215, "SRX2768765", "SRS2152474", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.9374, null, 0.14185, null, 0.67665, null, 0.47249, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42210, "SRR5485628", "SRX2768764", "SRS2152473", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "N 5.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "N 5.5.2", "N 5.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz", "fastq fastq", 2097386100.0, 20973861.0, "HI.4079.001.Index 21.N R1.fastq.gz", "0:100 1:0", "A:551586521;C:479609380;G:467572413;T:598246436;N:371350", 100, 0, null, null, 551586521, 479609380, 467572413, 598246436, 371350, "SRX2768764", "SRS2152473", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93984, null, 0.13949, null, 0.68219, null, 0.46921, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42211, "SRR5485627", "SRX2768763", "SRS2152472", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "O 5.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "O 5.20.2", "O 5.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz", "fastq fastq", 2003835800.0, 20038358.0, "HI.4079.001.Index 23.O R1.fastq.gz", "0:100 1:0", "A:529075084;C:456810826;G:444441300;T:573155538;N:353052", 100, 0, null, null, 529075084, 456810826, 444441300, 573155538, 353052, "SRX2768763", "SRS2152472", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93635, null, 0.15287, null, 0.67712, null, 0.45807, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42212, "SRR5485626", "SRX2768762", "SRS2152471", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "P 5.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "P 5.0.14", "P 5.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz", "fastq fastq", 1799355500.0, 17993555.0, "HI.4079.001.Index 27.P R1.fastq.gz", "0:100 1:0", "A:485156399;C:399414298;G:389730888;T:524733869;N:320046", 100, 0, null, null, 485156399, 399414298, 389730888, 524733869, 320046, "SRX2768762", "SRS2152471", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92813, null, 0.15749, null, 0.67943, null, 0.47424, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42213, "SRR5485625", "SRX2768761", "SRS2152470", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "Q 5.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "Q 5.5.14", "Q 5.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz", "fastq fastq", 2260494100.0, 22604941.0, "HI.4079.001.Index 2.Q R1.fastq.gz", "0:100 1:0", "A:602519260;C:506296484;G:495685951;T:655587703;N:404702", 100, 0, null, null, 602519260, 506296484, 495685951, 655587703, 404702, "SRX2768761", "SRS2152470", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92524, null, 0.14979, null, 0.6859, null, 0.47957, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42214, "SRR5485624", "SRX2768760", "SRS2152469", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "R 5.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "R 5.20.14", "R 5.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz", "fastq fastq", 1975297900.0, 19752979.0, "HI.4079.001.Index 13.R R1.fastq.gz", "0:100 1:0", "A:527732232;C:440160233;G:430962427;T:576091914;N:351094", 100, 0, null, null, 527732232, 440160233, 430962427, 576091914, 351094, "SRX2768760", "SRS2152469", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92785, null, 0.15864, null, 0.6814, null, 0.47773, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42215, "SRR5485623", "SRX2768759", "SRS2152468", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "S 6.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "S 6.0.2", "S 6.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz", "fastq fastq", 2690628500.0, 26906285.0, "HI.4079.001.Index 6.S R1.fastq.gz", "0:100 1:0", "A:713021693;C:609779787;G:594591832;T:772745072;N:490116", 100, 0, null, null, 713021693, 609779787, 594591832, 772745072, 490116, "SRX2768759", "SRS2152468", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93405, null, 0.15472, null, 0.68505, null, 0.45796, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42216, "SRR5485622", "SRX2768758", "SRS2152466", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "T 6.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "T 6.5.2", "T 6.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz", "fastq fastq", 1949043500.0, 19490435.0, "HI.4079.001.Index 15.T R1.fastq.gz", "0:100 1:0", "A:515794596;C:441198348;G:430323928;T:561379111;N:347517", 100, 0, null, null, 515794596, 441198348, 430323928, 561379111, 347517, "SRX2768758", "SRS2152466", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93579, null, 0.16207, null, 0.68473, null, 0.44993, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42217, "SRR5485621", "SRX2768757", "SRS2152467", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "U 6.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "U 6.20.2", "U 6.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz", "fastq fastq", 1754851900.0, 17548519.0, "HI.4079.001.Index 7.U R1.fastq.gz", "0:100 1:0", "A:464191451;C:397313933;G:387262108;T:505777499;N:306909", 100, 0, null, null, 464191451, 397313933, 387262108, 505777499, 306909, "SRX2768757", "SRS2152467", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93016, null, 0.16163, null, 0.68329, null, 0.47088, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42218, "SRR5485620", "SRX2768756", "SRS2152463", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "V 6.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "V 6.0.14", "V 6.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz", "fastq fastq", 2027423200.0, 20274232.0, "HI.4079.001.Index 18.V R1.fastq.gz", "0:100 1:0", "A:542440452;C:449399743;G:440389586;T:594839784;N:353635", 100, 0, null, null, 542440452, 449399743, 440389586, 594839784, 353635, "SRX2768756", "SRS2152463", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92441, null, 0.16974, null, 0.6842, null, 0.48209, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42219, "SRR5485619", "SRX2768755", "SRS2152464", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "W 6.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "W 6.5.14", "W 6.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz", "fastq fastq", 2139528300.0, 21395283.0, "HI.4079.001.Index 14.W R1.fastq.gz", "0:100 1:0", "A:569259910;C:478055273;G:469309420;T:622525486;N:378211", 100, 0, null, null, 569259910, 478055273, 469309420, 622525486, 378211, "SRX2768755", "SRS2152464", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92551, null, 0.15358, null, 0.68136, null, 0.47093, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42220, "SRR5485618", "SRX2768754", "SRS2152465", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0 5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "X 6.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "X 6.20.14", "X 6.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz", "fastq fastq", 1768110400.0, 17681104.0, "HI.4079.001.Index 16.X R1.fastq.gz", "0:100 1:0", "A:472810124;C:392555880;G:382616900;T:519817796;N:309700", 100, 0, null, null, 472810124, 392555880, 382616900, 519817796, 309700, "SRX2768754", "SRS2152465", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92486, null, 0.16073, null, 0.69041, null, 0.48403, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42525, "SRR5687196", "SRX2921961", "SRS2287821", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg5 2", "GSM2670727", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg5 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670727", "GSM2670727: GFPneg5 2; Danio rerio; RNA Seq", "GSM2670727", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670727", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive5set2_GTGAAA_L001_R1_001.fastq.gz GFPnegaitive5set2_GTGAAA_L001_R2_001.fastq.gz", "fastq fastq", 1952022216.0, 3158612.0, "GSM2670727 r1", "0:309 1:309", "A:607016523;C:396466091;G:392683679;T:555854857;N:1066", 309, 309, null, null, 607016523, 396466091, 392683679, 555854857, 1066, "SRX2921961", "SRS2287821", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.68529, 0.70068, 0.12269, 0.12678, 0.84133, 0.856, 0.71177, 0.82957, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42526, "SRR5687195", "SRX2921960", "SRS2287820", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg2 2", "GSM2670726", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg2 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670726", "GSM2670726: GFPneg2 2; Danio rerio; RNA Seq", "GSM2670726", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670726", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive2set2_ATTCCT_L001_R1_001.fastq.gz GFPnegaitive2set2_ATTCCT_L001_R2_001.fastq.gz", "fastq fastq", 1811912964.0, 2931898.0, "GSM2670726 r1", "0:309 1:309", "A:578442167;C:369836482;G:350128044;T:513498823;N:7448", 309, 309, null, null, 578442167, 369836482, 350128044, 513498823, 7448, "SRX2921960", "SRS2287820", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.64969, 0.66677, 0.08798, 0.08966, 0.87984, 0.88684, 0.88277, 0.87474, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42527, "SRR5687194", "SRX2921959", "SRS2287818", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg2", "GSM2670725", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670725", "GSM2670725: GFPneg2; Danio rerio; RNA Seq", "GSM2670725", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670725", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive2_CAGATC_L001_R1_001.fastq.gz GFPnegaitive2_CAGATC_L001_R2_001.fastq.gz", "fastq fastq", 1718976888.0, 2781516.0, "GSM2670725 r1", "0:309 1:309", "A:529099301;C:352155163;G:350456178;T:487264195;N:2051", 309, 309, null, null, 529099301, 352155163, 350456178, 487264195, 2051, "SRX2921959", "SRS2287818", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.71906, 0.72599, 0.20211, 0.20881, 0.77761, 0.79289, 0.65883, 0.66469, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42528, "SRR5687193", "SRX2921958", "SRS2287817", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPneg1", "GSM2670724", null, "tissue:Zebrafish retinal cells not rods|cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GFPneg1", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal cells not rods", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:non rod retinal cells|genotype/variation:XOPS:eGFP|cell type:GFP ; FACS sorted non rods from retina", "GSM2670724", "GSM2670724: GFPneg1; Danio rerio; RNA Seq", "GSM2670724", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670724", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPnegaitive1_CGATGT_L001_R1_001.fastq.gz GFPnegaitive1_CGATGT_L001_R2_001.fastq.gz", "fastq fastq", 2018776104.0, 3266628.0, "GSM2670724 r1", "0:309 1:309", "A:608896808;C:414729064;G:413070681;T:582077754;N:1797", 309, 309, null, null, 608896808, 414729064, 413070681, 582077754, 1797, "SRX2921958", "SRS2287817", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.72164, 0.72585, 0.19987, 0.20795, 0.78196, 0.80505, 0.65069, 0.64958, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42529, "SRR5687192", "SRX2921957", "SRS2287816", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos5 2", "GSM2670723", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos5 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670723", "GSM2670723: GFPpos5 2; Danio rerio; RNA Seq", "GSM2670723", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670723", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive5set2_GTCCGC_L001_R1_001.fastq.gz GFPpositive5set2_GTCCGC_L001_R2_001.fastq.gz", "fastq fastq", 1951035888.0, 3157016.0, "GSM2670723 r1", "0:309 1:309", "A:601202476;C:409815484;G:396381725;T:543631225;N:4978", 309, 309, null, null, 601202476, 409815484, 396381725, 543631225, 4978, "SRX2921957", "SRS2287816", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.66385, 0.68047, 0.17016, 0.1787, 0.82327, 0.83437, 0.66766, 0.66412, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42530, "SRR5687191", "SRX2921956", "SRS2287815", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos2 2", "GSM2670722", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos2 2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670722", "GSM2670722: GFPpos2 2; Danio rerio; RNA Seq", "GSM2670722", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670722", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive2set2_ACTGAT_L001_R1_001.fastq.gz GFPpositive2set2_ACTGAT_L001_R2_001.fastq.gz", "fastq fastq", 1756145880.0, 2841660.0, "GSM2670722 r1", "0:309 1:309", "A:564701465;C:354907068;G:340547873;T:495986512;N:2962", 309, 309, null, null, 564701465, 354907068, 340547873, 495986512, 2962, "SRX2921956", "SRS2287815", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.57879, 0.59269, 0.16217, 0.16717, 0.85516, 0.86277, 0.7228, 0.72512, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42531, "SRR5687190", "SRX2921955", "SRS2287814", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos2", "GSM2670721", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos2", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670721", "GSM2670721: GFPpos2; Danio rerio; RNA Seq", "GSM2670721", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670721", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive2_CCGTCC_L001_R1_001.fastq.gz GFPpositive2_CCGTCC_L001_R2_001.fastq.gz", "fastq fastq", 1812864684.0, 2933438.0, "GSM2670721 r1", "0:309 1:309", "A:549595811;C:382846743;G:374776217;T:505641489;N:4424", 309, 309, null, null, 549595811, 382846743, 374776217, 505641489, 4424, "SRX2921955", "SRS2287814", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.62676, 0.64046, 0.22945, 0.24228, 0.81268, 0.82574, 0.60502, 0.60668, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [42532, "SRR5687189", "SRX2921954", "SRS2287813", "SRP109268", "PRJNA390613", "Transcripts within Rod Photoreceptors of the Zebrafish Retina", "GSE100062", "Transcriptome Analysis", "Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish an important animal model for vision science. Methods: Zebrafish rods and non rod retinal cells of the XOPS:eGFP transgenic line were separated by cell dissociation and fluorescence activated cell sorting FACS followed by RNA seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01 597 transcripts were upregulated in rods vs. non rod retinal cells and 1032 were downregulated. 13 324 total transcripts were detected in rods including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA seq dataset describing the rod transcriptome of the zebrafish which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Overall design: 8 samples analyzed: 4 GFP+ FACS sorted rods 4 GFP FACS sorted non rods from retina; the two retinas from each of four fish contributed to each sample.", null, "pubmed:29422031", null, "GFPpos1", "GSM2670720", null, "tissue:Zebrafish retinal rod photoreceptors|cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GFPpos1", "Quality trimmed with Sickle https://github.com/najoshi/sickle Paired reads were overlapped with FLASH https://ccb.jhu.edu/software/FLASH/ Overlapped reads were against the Danio rerio reference using BWA http://bio bwa.sourceforge.net/ BAMs were sorted using SAMtools http://samtools.sourceforge.net/ Reads were counted by feature using htseq count http://www huber.embl.de/HTSeq/doc/count.html Counts were analyzed and differentially expressed genes were identified with R and edgeR https://bioconductor.org/packages/release/bioc/html/edgeR.html Genome build: Zv9.75 Supplementary files format and content: Read count data from HTSeq; EdgeR analysis results with annotation", "Zebrafish retinal rod photoreceptors", "Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin Fisher ThermoScientific and 0.001% papain Sigma for 10 minutes at 37\u00b0C. Dissociation was stopped by the addition of fetal bovine serum 10% v/v final concentration. Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 \u00b5L phosphate buffered pH 6.5 saline PBS and immediately FACS sorted. GFP+ vs. GFP retinal cells were sorted using a FACSAria flow cytometer using the 488 nm laser and FITC fluorescence filter and the 70 \u00b5m nozzle. Some cells were collected for fluorescence microscopy or for post sort FACS analysis. For RNA seq or qPCR GFP+ and GFP cells were collected separately in a final volume of 100 \u00b5L of the FACS sheath fluid and RNA was immediately extracted.", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "Zebrafish XOPS:eGFP transgenic line were on a 14:10 light:dark cycle in recirculating monitored system water housed and propagated according to The Zebrafish Book Westerfield.", "cell type:rod photoreceptors|genotype/variation:XOPS:eGFP|cell type:GFP+; FACS sorted rods", "GSM2670720", "GSM2670720: GFPpos1; Danio rerio; RNA Seq", "GSM2670720", null, "1", "RNA was extracted from tissue samples using the NucleoSpin\u00ae\u00a0RNA kit Macherey Nagel using the manufacturer\u2019s protocol quantified and quality checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA seq had an RNA integrity number RIN > 8.0 and experimental design was such that GFP+ cells or GFP cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample and provided to the University of Idaho\u2019s Institute for Bioinformatics and Evolutionary Studies IBEST Genomics Core for RNA amplification and the generation of cDNA. Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation\u00ae RNA Seq System V2 NuGEN and sequencing performed on an Illumina San Diego CA MiSeq. Four replicates from four different fish were sequenced Fig. 1A. Mapping percentages ranged from 97.0% to 97.4% per sample and sequencing depth ranged from 2 781 516 to 3 480 515 reads per sample.", "GEO Accession:GSM2670720", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP109268", null, null, "GFPpositive1_TGACCA_L001_R1_001.fastq.gz GFPpositive1_TGACCA_L001_R2_001.fastq.gz", "fastq fastq", 2150958270.0, 3480515.0, "GSM2670720 r1", "0:309 1:309", "A:654306402;C:442036224;G:437971529;T:616642033;N:2082", 309, 309, null, null, 654306402, 442036224, 437971529, 616642033, 2082, "SRX2921954", "SRS2287813", "SRA574861", "GEO", "Biological Sciences, University of Idaho", 2, 0.65859, 0.66368, 0.295, 0.31011, 0.79324, 0.81454, 0.55325, 0.5597, 309, 309, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-06-15", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43465, "SRR6888838", "SRX3839388", "SRS3086676", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 WKM Scar", "GSM3065994", null, "tissue:WKM single cells|cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "P2 WKM Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "WKM single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "GSM3065994", "GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq", "GSM3065994", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-WKM-001-Scar_R1.fastq.gz P2-WKM-001-Scar_R2.fastq.gz", "fastq fastq", 344288293.0, 2265619.0, "GSM3065994 r1", "0:75.98 1:75.98", "A:60840077;C:100295730;G:126071444;T:57044397;N:36645", 75, 75, null, null, 60840077, 100295730, 126071444, 57044397, 36645, "SRX3839388", "SRS3086676", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.0007, 0.00458, 0.00047, 0.00268, 0.99971, 0.99669, 0.37837, 0.42452, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [43466, "SRR6888839", "SRX3839388", "SRS3086676", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 WKM Scar", "GSM3065994", null, "tissue:WKM single cells|cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "P2 WKM Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "WKM single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:WKM|sorted plates:2", "GSM3065994", "GSM3065994: P2 WKM Scar; Danio rerio; RNA Seq", "GSM3065994", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-WKM-002-Scar_R1.fastq.gz P2-WKM-002-Scar_R2.fastq.gz", "fastq fastq", 717066879.0, 4719933.0, "GSM3065994 r2", "0:75.98 1:75.94", "A:126563252;C:209265530;G:262732780;T:118432095;N:73222", 75, 75, null, null, 126563252, 209265530, 262732780, 118432095, 73222, "SRX3839388", "SRS3086676", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00063, 0.1196, 0.00034, 0.0666, 0.99977, 0.99598, 0.23529, 0.45161, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [43467, "SRR6888837", "SRX3839387", "SRS3086675", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 right midbrain Scar", "GSM3065993", null, "tissue:right midbrain single cells|cas9 injection:protein|FISH id:P2|organ:right midbrain|sorted plates:1", "P2 right midbrain Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right midbrain single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:right midbrain|sorted plates:1", "GSM3065993", "GSM3065993: P2 right midbrain Scar; Danio rerio; RNA Seq", "GSM3065993", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Midbrain-right-p01-Scar_R1.fastq.gz P2-Midbrain-right-p01-Scar_R2.fastq.gz", "fastq fastq", 152826307.0, 1005857.0, "GSM3065993 r1", "0:75.98 1:75.95", "A:27775284;C:45270196;G:56312550;T:23417130;N:51147", 75, 75, null, null, 27775284, 45270196, 56312550, 23417130, 51147, "SRX3839387", "SRS3086675", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00023, 0.00037, 0.0002, 0.00032, 0.99993, 0.99985, 0.0, 0.42857, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [43468, "SRR6888836", "SRX3839386", "SRS3086673", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 left midbrain Scar", "GSM3065992", null, "tissue:left midbrain single cells|cas9 injection:protein|FISH id:P2|organ:left midbrain|sorted plates:1", "P2 left midbrain Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left midbrain single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:left midbrain|sorted plates:1", "GSM3065992", "GSM3065992: P2 left midbrain Scar; Danio rerio; RNA Seq", "GSM3065992", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Midbrain-left-p01-Scar_R2.fastq.gz P2-Midbrain-left-p01-Scar_R1.fastq.gz", "fastq fastq", 98906805.0, 650967.0, "GSM3065992 r1", "0:75.98 1:75.96", "A:17838466;C:29265024;G:36491674;T:15282661;N:28980", 75, 75, null, null, 17838466, 29265024, 36491674, 15282661, 28980, "SRX3839386", "SRS3086673", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 1e-05, 1e-05, 0.0, 0.0, 0.99997, 0.99997, 0.0, 0.0, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [43469, "SRR6888835", "SRX3839385", "SRS3086671", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 forebrain Scar", "GSM3065991", null, "tissue:forebrain single cells|cas9 injection:protein|FISH id:P2|organ:forebrain|sorted plates:1", "P2 forebrain Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "forebrain single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:forebrain|sorted plates:1", "GSM3065991", "GSM3065991: P2 forebrain Scar; Danio rerio; RNA Seq", "GSM3065991", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Forebrain-p01-Scar_R2.fastq.gz P2-Forebrain-p01-Scar_R1.fastq.gz", "fastq fastq", 39304298.0, 259048.0, "GSM3065991 r1", "0:75.93 1:75.80", "A:7719394;C:11234773;G:13950579;T:6398707;N:845", 75, 75, null, null, 7719394, 11234773, 13950579, 6398707, 845, "SRX3839385", "SRS3086671", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00783, 0.00436, 0.00683, 0.00405, 0.99989, 0.99945, 0.01265, 0.48148, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Brain", "Nervous System"], [43470, "SRR6888834", "SRX3839384", "SRS3086672", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 right eye Scar", "GSM3065990", null, "tissue:right eye single cells|cas9 injection:protein|FISH id:P2|organ:right eye|sorted plates:1", "P2 right eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "right eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:right eye|sorted plates:1", "GSM3065990", "GSM3065990: P2 right eye Scar; Danio rerio; RNA Seq", "GSM3065990", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065990", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Eye-right-p01-Scar_R1.fastq.gz P2-Eye-right-p01-Scar_R2.fastq.gz", "fastq fastq", 39029616.0, 257084.0, "GSM3065990 r1", "0:75.94 1:75.88", "A:7556894;C:11070936;G:13942796;T:6447595;N:11395", 75, 75, null, null, 7556894, 11070936, 13942796, 6447595, 11395, "SRX3839384", "SRS3086672", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00367, 0.00526, 0.00323, 0.00449, 0.9988, 0.99813, 0.31168, 0.32231, 76, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43471, "SRR6888833", "SRX3839383", "SRS3086669", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 left eye Scar", "GSM3065989", null, "tissue:left eye single cells|cas9 injection:protein|FISH id:P2|organ:left eye|sorted plates:1", "P2 left eye Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "left eye single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:left eye|sorted plates:1", "GSM3065989", "GSM3065989: P2 left eye Scar; Danio rerio; RNA Seq", "GSM3065989", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065989", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-Eye-left-p01-Scar_R2.fastq.gz P2-Eye-left-p01-Scar_R1.fastq.gz", "fastq fastq", 38948398.0, 256405.0, "GSM3065989 r1", "0:75.98 1:75.92", "A:7098142;C:11543244;G:14180784;T:6112258;N:13970", 75, 75, null, null, 7098142, 11543244, 14180784, 6112258, 13970, "SRX3839383", "SRS3086669", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00055, 0.00086, 0.00048, 0.00075, 0.99979, 0.99971, 0.63636, 0.375, 75, 75, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Eye", "Sensory System"], [43472, "SRR6888831", "SRX3839382", "SRS3086668", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 cfin vent Scar", "GSM3065988", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P2 cfin vent Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065988", "GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq", "GSM3065988", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Vent-003-Scar_R1.fastq.gz P2-CFin-Vent-003-Scar_R2.fastq.gz", "fastq fastq", 344793287.0, 2269321.0, "GSM3065988 r1", "0:75.99 1:75.95", "A:61565924;C:101344805;G:127059615;T:54785853;N:37090", 75, 75, null, null, 61565924, 101344805, 127059615, 54785853, 37090, "SRX3839382", "SRS3086668", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00015, 0.00029, 0.00012, 0.00017, 0.99993, 0.99977, 0.33333, 0.58823, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43473, "SRR6888832", "SRX3839382", "SRS3086668", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P2 cfin vent Scar", "GSM3065988", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P2 cfin vent Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065988", "GSM3065988: P2 cfin vent Scar; Danio rerio; RNA Seq", "GSM3065988", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065988", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Vent-004-Scar_R1.fastq.gz P2-CFin-Vent-004-Scar_R2.fastq.gz", "fastq fastq", 110701966.0, 728490.0, "GSM3065988 r2", "0:75.99 1:75.97", "A:19507928;C:32552811;G:40930271;T:17699467;N:11489", 75, 75, null, null, 19507928, 32552811, 40930271, 17699467, 11489, "SRX3839382", "SRS3086668", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00021, 0.0004, 0.00015, 0.00031, 0.99991, 0.99981, 1.0, 0.84615, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43474, "SRR6888829", "SRX3839381", "SRS3086670", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P1 cfin dorsal Scar", "GSM3065987", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P1 cfin dorsal Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065987", "GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq", "GSM3065987", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. 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For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "P1 cfin dorsal Scar", "GSM3065987", null, "tissue:primary fin single cells|cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "P1 cfin dorsal Scar", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files.", "primary fin single cells", null, "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", null, "cas9 injection:protein|FISH id:P2|organ:primary fin|sorted plates:2", "GSM3065987", "GSM3065987: P1 cfin dorsal Scar; Danio rerio; RNA Seq", "GSM3065987", null, "1", "post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters", "GEO Accession:GSM3065987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP116018", null, null, "P2-CFin-Dors-004-Scar_R1.fastq.gz P2-CFin-Dors-004-Scar_R2.fastq.gz", "fastq fastq", 856597590.0, 5637115.0, "GSM3065987 r2", "0:75.99 1:75.97", "A:151359975;C:251587454;G:317011744;T:136549208;N:89209", 75, 75, null, null, 151359975, 251587454, 317011744, 136549208, 89209, "SRX3839381", "SRS3086670", "SRA602108", "GEO", "AVO, Hubrecht Institue", 2, 0.00027, 0.00065, 0.00016, 0.00039, 0.99975, 0.99951, 0.29411, 0.53658, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "random_priming", "trueseq", "sc", "other_seq", "scartrace", null, "Netherlands", "2018-03-23", "Undetermined", "Multi-stage", "Fin", "Surface Structure"], [43476, "SRR6020446", "SRX3171493", "SRS2501302", "SRP116018", "PRJNA399711", "Whole organism clone tracing using single cell sequencing", "GSE102990", "Transcriptome Analysis", "We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. 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For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. 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Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. 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Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. 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For each cell we provide libraries with transcritpome and with clonal information respectively.", null, "pubmed:29590089", null, "R5 sec Trans", "GSM2776988", null, "source name:secondary fin single cells|cas9 injection:mRNA|FISH id:R5|tissue:secondary fin|sorted plates:6", "R5 sec Trans", "In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. 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