run_metadata: 71607

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
71607	SRR21782745	SRX17777231	SRS15303485	SRP400712	PRJNA886442	Tulp1 deficiency causes early onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish	GSE214642	Transcriptome Analysis	Mutations in TUB like protein 1 TULP1 are associated with severe early onset retinal degeneration in humans. However the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish namely tulp1a and tulp1b. Here we generated the single knockout tulp1a / and tulp1b / and double knockout tulp1 dKO models in zebrafish. Knockout of tulp1a results in the mislocalization of UV cone opsins and the degeneration of UV cones specifically while knockout of tulp1b results in mislocalization of rod opsins and rod cone degeneration. In the tulp1 dKO zebrafish mislocalization of opsins was present in all types of photoreceptors and severe degeneration was observed at a very early age mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1 dKO retinas. RNA seq analysis showed that the expression of tektin2 tekt2 a ciliary and flagellar microtubule structural component was downregulated in the tulp1 dKO zebrafish. Dual luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. Additionally ferroptosis might be activated in the tulp1 dKO zebrafish as suggested by the up regulation of genes related to the ferroptosis pathway the shrinkage of mitochondria reduction or disappearance of mitochondria cristae and the iron and lipid droplet deposition in the retina of tulp1 dKO zebrafish. In conclusion our study establishes an appropriate zebrafish model for TULP1 associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2 which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early onset retinal degeneration. Overall design: Comparative gene expression profiling analysis of RNA seq data for wt and tulp1a&tulp1b zebrafish.		pubmed:36396940		WT1	GSM6613552		source name:head\|tissue:head\|strain:AB\|genotype:wild type\|developmental stage:4 dpf	WT1	Illumina Novaseq 6000 software used for basecalling. Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing poly N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 and paired end clean reads were aligned to the reference genome using Hisat2. TPM conversion was performed to obtain the standardized gene/transcript expression level. Assembly: GRCz11 Supplementary files format and content: * TPM.csv: Comma separated text files include TPM values.	head		The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.		tissue:head\|strain:AB\|genotype:wild type\|developmental stage:4 dpf	GSM6613552	GSM6613552: WT1; Danio rerio; RNA Seq	GSM6613552 r1	GSM6613552	1	The heads of zebrafish larvae were dissected for RNA extraction. Total RNA was extracted with the RNA isolater Total RNA Extraction Reagent. RNA libraries were prepared for sequencing using standard Illumina protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP400712			L1EFA141669_WT1.R1.raw.fastq.gz L1EFA141669_WT1.R2.raw.fastq.gz	fastq fastq	7238862688.0	23969744.0	GSM6613552 r1	0:151 1:151	A:1972024445;C:1640211955;G:1685856317;T:1940696938;N:73033	151	151			1972024445	1640211955	1685856317	1940696938	73033	SRX17777231	SRS15303485	SRA1511428	Huazhong University of Science and Technology	Huazhong University of Science and Technology	2	0.9253	0.92638	0.11986	0.11995	0.6521	0.6519	0.47312	0.47348	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		China	2022-10-02	Larval	Larval	Head	Nervous System