run_metadata: 30667

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
30667	SRR28146893	SRX23777733	SRS20602698	SRP492278	PRJNA1081795	Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a	GSE260453	Transcriptome Analysis	The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However whether viral infection can affect the hypoxia response is still largely unknown. In this study we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination leading to their stabilization and subsequent enhancement of target gene expression. Moreover treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB USA #E7530L following manufacturer's protocol In order to ensure the quality of information analysis the software fastp was used to remove the splice sequences filter the low quality N bases indicating that the base information could not be determined and obtain high quality clean data. clean data and the number of bases and sequences of the clean data were counted. At the same time GC Q20 Q30 content of the clean data were calculated GenePlus Beijing China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.		pubmed:39601573		zebrafish larvae svcv1	GSM8117448		source name:larvae\|tissue:larvae\|genotype:WT\|treatment:svcv infection\|geo loc name:missing\|collection date:missing	zebrafish larvae svcv1	Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample	larvae		Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB USA #E7530L accordingly to the manufacturer’s protocol and index codes were added to assign sequences to each sample.		tissue:larvae\|genotype:WT\|treatment:svcv infection	GSM8117448	GSM8117448: zebrafish larvae svcv1; Danio rerio; RNA Seq	GSM8117448 r1	GSM8117448	1	Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB USA #E7530L accordingly to the manufacturer's protocol and index codes were added to assign sequences to each sample.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP492278			svcv-1_1.fq.gz svcv-1_2.fq.gz	fastq fastq	10699844400.0	35666148.0	GSM8117448 r1	0:150 1:150	A:2874259238;C:2464699540;G:2474659412;T:2883944709;N:2281501	150	150			2874259238	2464699540	2474659412	2883944709	2281501	SRX23777733	SRS20602698	SRA1812384	????????????	中国科学院水生生物研究所	2	0.94238	0.941	0.11297	0.11345	0.65218	0.65518	0.47212	0.47861	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	nebnext	bulk	unknown	unknown		China	2024-02-28	Larval	Larval	Undetermined	Undetermined