run_metadata: 38302

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
38302	SRR1695730	SRX798420	SRS781712	SRP050879	PRJNA269540	zebrafish transciptsome sequencing	PRJNA269540	Other	we aimed to calculate the expression level of some special genes				Testis from Danio rerio	testis of zebrafish		strain:AB\|dev stage:adult\|sex:male\|tissue:testis\|biomaterial provider:zebrafish facilities of the Institute of Hydrobiology Chinese Academy of Sciences\|BioSampleModel:Model organism or animal									RNA seq of zebrafish testis	testis of zebrafish	Zebrafish facilities of the Institute of Hydrobiology Chinese Academy of Sciences	Wild type zebrafish from an AB background were maintained in the zebrafish facilities of the Institute of Hydrobiology Chinese Academy of Sciences. Testis of adult is collected for RNA extraction. Total RNA extraction was performed with TRIZOL reagents from Takara following the manufacturer’s instructions. Total RNA contents were measured using the NanoDrop 2000. Then 5 μg total RNA was used for mRNA isolation with oligo dT magnetic beads and fragmented into small pieces in fragmentation buffer at 70°C for 4 min before cDNA synthesis. First strand cDNA was synthesized from the cleaved RNA using SuperScript II reverse transcriptase and random hexamer primers followed by second strand cDNA synthesis using DNA polymerase I and RNaseH. post purification with a QIAquick PCR Purification Kit Qiagen Dusseldorf Germany the double stranded cDNA was treated to repair ends by T4 DNA polymerase Klenow enzyme and T4 polynucleotide kinase NEB. This was followed by addition of a single A base using Klenow exo polymerase and ligation with an adapter using DNA ligase NEB. post ligation the DNA was purified using a QIAquick PCR Purification Kit. PCR amplification with 10 to 12 cycles was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments. post purification using a QIAquick PCR Purification Kit the product was dissolved in 30 µL of Qiagen EB buffer. These DNA fragments represented the designated mRNA library. The cDNA library was quantified with Qubit Invitrogen and a cluster of the DNA fragment was amplified using bridge PCR on the surface of a flow cell chip. Multiplexed libraries were sequenced for 101bp at both ends using an Illumina HiSeqTM 2000 platform.			RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP050879			Zebrafish_256-T14-VI_good_1.fq.gz Zebrafish_256-T14-VI_good_2.fq.gz	fastq fastq	5252571430.0	26005174.0	testis of zebrafish	0:100.99 1:100.99	A:1353125230;C:1273042497;G:1273793183;T:1350916239;N:1694281	100	100			1353125230	1273042497	1273793183	1350916239	1694281	SRX798420	SRS781712	SRA210676	CAS\|systematic evolution	Institute of Hydrobiology, Chinese Academy of sciences	2	0.93036	0.93332	0.09196	0.09372	0.64559	0.64806	0.48865	0.48746	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		China	2015-09-23	Adult	Adult	Gonad	Reproductive System