run_metadata: 31477

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
31477	SRR28362825	SRX23967981	SRS20767212	SRP495638	PRJNA1088730	Effects of noxo1a deficiency on gene expression in zebrafish larvae upon exposure to cold warm stress	PRJNA1088730	Other	Exposure of fish to cold warm stress was reported to elicit ROS generation and subsequent tissue damage. On the other hand ROS signaling is essential for many physiological functions of the organism. As a NADPH oxidase NOX organizer deficiency of Noxo1a is expected to decrease the content of hydrogen peroxide in fish tissue upon exposure to cold warm stress. In this study the effect on Noxo1a deficiency on gene expression in zebrafish larvae under cold warm stress was characterized by RNA sequencing.				WT cs#2	WT cs#2		strain:AB strain\|dev stage:Larvae\|collection date:2023 03 05\|geo loc name:China: Wuhan\|sex:not determined\|tissue:Whole body\|genotype:Wild type\|treatment:Exposed to 10 °C for 12 h\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal									WT cs#2	WT cs#2	WT cs#2	One microgram total RNA from each sample was used as the beginning material for sequencing library construction. Each treatment included 4 biological replicates. The NEBNext rRNA Depletion Kit was used for rRNA depletion. post rRNA depletion Agencourt RNAClean XP Beads from Beckman Coulter were used for RNA purification. Then the NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used for RNA fragmentation first and second strand cDNA synthesis double stranded cDNA end repair. Double strand cDNAs were purified using the Agencourt AMPure XP from Beckman Coulter and ligated to adaptors of NEBNext Multiplex Oligos for Illumina. Finally the Q5 Hot Start HiFi PCR Master Mix was used for PCR enrichment of the adaptor ligated DNA. The concentration and quality of the constructed sequencing libraries were measured by using the Agilent High Sensitivity DNA Kit and a Bioanalyzer 2100 from Agilent Technologies. The libraries were submitted to 51 bp single end high throughput sequencing by the Center for Advanced Technology CAT of the University of California San Francisco using Hiseq 3000.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP495638			wt-cs-2_S36_L004_R1_001.fastq.gz wt-cs-2_S36_L004_R2_001.fastq.gz	fastq fastq	7863905100.0	26213017.0	wt cs 2 S36 L004 R1 001.fastq.gz	0:150 1:150	A:2095810379;C:1826144395;G:1861582031;T:2079957538;N:410757	150	150			2095810379	1826144395	1861582031	2079957538	410757	SRX23967981	SRS20767212	SRA1825819	Chinese Academy of Sciences\|Institute of Hydrobiology	Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown		China	2024-03-16	Larval	Larval	Trunk	Surface Structure