run_metadata: 10162

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
10162	ERR5385018	ERX5169944	ERS5845163	ERP127328	PRJEB43370	RNA seq of whole zebrafish embryos at 6 and 10hpf	E-MTAB-10167	Other	RNA seq was performed to reveal the RNA expression profile at two different stages shield and tail bud stage in the embryogenesis of zebrafish wild type strain AB. Zebrafish embryos were collected at the shield stage and tail bud stage which correspond to 6 hpf and 10 hpf respectively. Total RNA was extracted with miRNeasy Mini Kit libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina and paired end sequencing was performed using NovaSeq 6000 Illumina.	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14		Protocols: Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage which correspond to 6 hpf and 10 hpf respectively. Total RNA was extracted with miRNeasy Mini Kit Qiagen 217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at 80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.	Danio rerio AB wildtype shield stage	SAMEA8158395	Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University	ENA first public:2021 07 01\|ENA last update:2021 07 01\|External Id:SAMEA8158395\|INSDC center alias:Department of Cellular Regulation Research Institute for Microbial Diseases Osaka University\|INSDC center name:Department of Cellular Regulation Research Institute for Microbial Diseases Osaka University\|INSDC first public:2021 07 01T00:11:10Z\|INSDC last update:2021 07 01T00:11:10Z\|INSDC status:public\|Submitter Id:E MTAB 10167:Danio rerio AB wildtype shield stage\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:gastrula shield\|genotype:wild type genotype\|organism part:whole organism\|sample name:E MTAB 10167:Danio rerio AB wildtype shield stage\|strain:AB									Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf	E MTAB 10167:Danio rerio AB wildtype shield stage p	Danio rerio AB wildtype shield stage p	RNA seq of whole zebrafish embryos at 6 and 10hpf	Zebrafish embryos obtained from wild type strain AB were collected at the shield stage and tail bud stage which correspond to 6 hpf and 10 hpf respectively. Total RNA was extracted with miRNeasy Mini Kit Qiagen 217004 according to the manufacturer's instructions. Quality of extracted RNA was assessed using the NanoDrop ND 1000 Spectrophotometer ThermoFisher Scientific and by agarose gel electrophoresis. Samples were stored at 80 ℃ Libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit Illumina according to the manufacturer's instructions.	Experimental Factor: developmental stage:gastrula shield	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP127328	Illumina NovaSeq 6000 paired end sequencing; RNA seq of whole zebrafish embryos at 6 and 10hpf	ENA FIRST PUBLIC:2022 01 14\|ENA LAST UPDATE:2022 01 14	6hpf_Zebrafish_R1.fastq.gz 6hpf_Zebrafish_R2.fastq.gz	fastq fastq	13564619564.0	67151582.0	E MTAB 10167:6hpf Zebrafish R	0:101 1:101	A:3600635755;C:3192954183;G:3191087455;T:3579609049;N:333122	101	101			3600635755	3192954183	3191087455	3579609049	333122	ERX5169944	ERS5845163	ERA3502311	Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University\|European Nucleotide Archive	Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University\|European Nucleotide Archive	2	0.95783	0.95972	0.08032	0.07998	0.75619	0.75694	0.468	0.48015	101	101	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		Japan	2021-07-01	Gastrula	Embryo	Whole Organism	All anatomical structures