{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["33278"], "units": {}, "query_ms": 9.864788997219875}