run_metadata: 33272

This data as json

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
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.		pubmed:39890032		Eye WT Female 2	GSM8406323		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 ≤ 0.05 and log2fold change ≥ \|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		RNA extraction was performed using the Zymo Quick RNA Miniprep kit with in column DNase 1 digestion step. RNA was eluted in 50µL 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		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 50µL 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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP520852			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			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		United States	2024-07-18	Undetermined	Multi-stage	Brain	Nervous System