run_metadata: 31531

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
31531	SRR28467113	SRX24070102	SRS20860624	SRP498043	PRJNA1091388	Danio rerio Raw sequence reads	PRJNA1091388	Whole Genome Sequencing	normal RNA seq of Danio rerio					BPG 3		strain:AB Wild type\|isolate:Zebrafish of BPG treatment group 3\|breed:no collected\|cultivar:no collected\|ecotype:Nanjing\|age:5 dpf stage:larval fish\|collection date:2023 02\|geo loc name:China: Nanjing\|sex:not applicable\|tissue:the whole body\|BioSampleModel:Model organism or animal									RNA Seq of Zebrafish larvae	ZXY BPG 3	ZXY BPG 3	Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software			RNA-Seq	TRANSCRIPTOMIC	PCR	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP498043			BPG3.raw_1.fastq.gz BPG3.raw_2.fastq.gz	fastq fastq	10077237000.0	33590790.0	BPG3.raw 1.fastq.gz	0:150 1:150	A:2739033278;C:2249842624;G:2379133275;T:2709150044;N:77779	150	150			2739033278	2249842624	2379133275	2709150044	77779	SRX24070102	SRS20860624	SRA1834298	Chinese Academy of Agricultural Sciences\|Institute of Quality Standards and Testing Technol	Chinese Academy of Agricultural Sciences	2	0.94306	0.94056	0.10748	0.10702	0.67653	0.67986	0.5156	0.50914	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		China	2024-03-27	Larval	Larval	Trunk	Surface Structure