run_metadata: 9716

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
9716	ERR3365995	ERX3390283	ERS3506631	ERP115705	PRJEB32960	RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type	E-MTAB-8029	Transcriptome Analysis	RNA was extracted from 5 dpf embyros with and without xxx c.386C>T p.Ser129Phe variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.	ENA FIRST PUBLIC:2019 07 19\|ENA LAST UPDATE:2019 06 10		Protocols: Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.	c.386C T het 5dpf whl3	SAMEA5702974	Medical College of Wisconsin	ENA FIRST PUBLIC:2019 07 19T04:04:05Z\|ENA LAST UPDATE:2019 06 10T11:46:52Z\|External Id:SAMEA5702974\|INSDC center name:Medical College of Wisconsin\|INSDC first public:2019 07 19T04:04:05Z\|INSDC last update:2019 06 10T11:46:52Z\|INSDC status:public\|Submitter Id:E MTAB 8029:c.386C T het 5dpf whl3\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:larval day 5\|genotype:wdr37 mutant c.386C>T p.Ser129Phe\|individual:mixed pool of 5 embryos\|organism part:whole organism\|sample name:E MTAB 8029:c.386C T het 5dpf whl3\|scientific name:Danio rerio									HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type	E MTAB 8029:c.386C T het 5dpf whl3 p	c.386C T het 5dpf whl3 p	RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type	Five dpf zebrafish embryos were genotyped. Three independent RNA samples were prepared for both WT and mutant with 5 embryos pooled for each sample. RNA samples were prepared using Direct zol™ RNA MiniPrep kit Zymo Research. TruSeq RNA Sample Prep Kit v2 was used with protocol TruSeq RNA Sample Preparation v2 Guide Part # 15026495 Rev. F.	Experimental Factor: genotype:wdr37 mutant c.386C>T p.Ser129Phe	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq X Ten		ERP115705	HiSeq X Ten paired end sequencing; RNA Seq of zebrafish embryos with wdr37 missense variant compared to wild type	ENA FIRST PUBLIC:2019 07 19\|ENA LAST UPDATE:2019 06 12\|instrument model:HiSeq X Ten	c386C-T-het-5dpf-whl-3_1.fastq.gz c386C-T-het-5dpf-whl-3_2.fastq.gz	fastq fastq	6059681642.0	20065171.0	E MTAB 8029:c386C T het 5dpf whl 3	0:151 1:151	A:1604034432;C:1423963595;G:1467519505;T:1563303018;N:861092	151	151			1604034432	1423963595	1467519505	1563303018	861092	ERX3390283	ERS3506631	ERA1993466	European Nucleotide Archive	European Nucleotide Archive	2	0.93301	0.9374	0.0658	0.06581	0.66681	0.68503	0.46139	0.47743	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown		Unknown	2019-06-10	Larval	Larval	Whole Organism	All anatomical structures