run_metadata: 73929

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
73929	SRR23286025	SRX19229346	SRS16634369	SRP420252	PRJNA929940	Transcriptomic Analysis of Zebrafish Larvae infected with Cyprinid Herpesvirus 3	PRJNA929940	Other	The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death.					CyHV 3 Infected and Mock Infected WT AB Zebrafish Larvae 3 dpf sampled at 1 2 and 3 dpi		strain:WT AB\|age:3 dpf stage:larvae\|sex:pooled male and female\|tissue:whole larvae\|BioSampleModel:Model organism or animal									CyHV 3 Infected WT AB Zebrafish Larvae 4 dpi Replicate 2	D4 I 2	D4 I 2	The goal of this experiment was to characterise the response to Cyprinid Herpesvirus 3 CyHV 3 infection in WT AB zebrafish larvae in terms of the interferon stimulated gene ISG upregulation and the potential involvement of programmed cell death. Zebrafish larvae were either infected with CyHV 3 or mock infected with PBS at three dpf. Larvae were sampled at 1 2 and 4 days post infection dpi. Samples were taken in triplicate at each time point each replicate consisted of five pooled larvae. For each sample immediately post euthanasia five whole larvae were lysed together in 700 μL QIAZol Qiagen and lysate was stored at 80C. post phase separation RNA was extracted from the aqueous layer as per RNeasy kit with on column DNase digestion. Samples were analysed by Agilent 2100 Bioanalyzer to confirm that all samples exhibited RIN values >9.5. RNA sequencing libraries were prepared using TruSeq Stranded mRNA kit Illumina as per manufacturers instructions. Sequencing was conducted using the Illumina NextSeq 500 System. Data consists of original raw output from RNAseq with no adapter or quality trimming .fastq fromat. Please refer to publication for further details.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	SINGLE	ILLUMINA	NextSeq 500		SRP420252			Zeb_D4_I_2.fastq.gz	fastq	1261376343.0	16699046.0	Zeb D4 I 2.fastq.gz	0:75.54 1:0	A:305088523;C:308891057;G:292935798;T:354388839;N:72126	75	0			305088523	308891057	292935798	354388839	72126	SRX19229346	SRS16634369	SRA1582637	University of Liege\|Faculty of Veterinary Medicine	University of Liege	1	0.8161		0.08611		0.66038		0.46493		75		B		usable mapping rate	illumina	nextseq	unknown	poly_a	trueseq	bulk	unknown	unknown		Belgium	2023-01-31	Larval	Larval	Whole Organism	All anatomical structures