run_metadata: 50949

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
50949	SRR8377249	SRX5187208	SRS4193610	SRP174644	PRJNA512103	Danio rerio amh mutant RNA Seq	PRJNA512103	Other	For 21dpf and 35dpf juvenile zebrafish trunk tissue was isolated by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. For adults ovary and testis was dissected separately from other tissues. Total RNA was extracted using the Ribopure Kit Thermo Fisher and polyA mRNA was enriched using Dynabeads Thermo Fisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex™ qRNA seq kit BIOO Scientific. Libraries were normalized to 2.3nM multiplexed and evaluated by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.		pubmed:31399485			WT test1		strain:AB\|age:adult\|sex:male\|tissue:testis\|biomaterial provider:Zebrafish Facility at the University of Oregon\|collected by:Yilin Yan\|replicate:biological replicate 1 wild type testis\|BioSampleModel:Model organism or animal									Danio rerio amh mutant RNA seq	WT test1	WT test1	Zebrafish were euthanized in Tricaine. We isolated gonad containing trunk of the animals by removing the anterior of the fish from just posterior of the pectoral fin and removing the caudal peduncle posterior to the anus. Trunks were individually homogenized in 200ul Trizol. Total RNA was extracted following Amores 2011. Total RNA was enriched for mRNA using Dynabeads Oligodt25 ThermoFisher. We constructed indexed strand specific cDNA sequencing libraries using the NEXTflex qRNA seq kit BIOO Scientific. Library concentrations were quantified using a Qubit fluorometer Life Technologies normalized to a concentration of 2.3nM and multiplexed. Prior to sequencing we further evaluated the quality of the multiplexed library by quantitative real time PCR using the Kapa Library Quantification Kit Kapa Biosystems. One lane of paired end 100 base pair bp sequencing was performed on an Illumina HiSeq 4000.			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP174644			WT_test1_R2.fq.gz WT_test1_R1.fq.gz	fastq fastq	2303992608.0	11405904.0	WT test1 R1.fq.gz	0:101 1:101	A:567633881;C:563967121;G:572235529;T:594400255;N:5755822	101	101			567633881	563967121	572235529	594400255	5755822	SRX5187208	SRS4193610	SRA827573	University of Oregon\|Biology	University of Oregon	2	0.80661	0.83085	0.17247	0.1314	0.69023	0.69094	0.39549	0.64674	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2019-09-06	Adult	Adult	Gonad	Reproductive System