run_metadata: 55325

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
55325	SRR10272860	SRX6986072	SRS5509254	SRP225457	PRJNA577338	Testes transcriptomes of Wild Type and Rbm46 KO mutants	PRJNA577338	Other	Molecular consequences of Rbm46 depletion in zebrafish germ cells using RNA seq				Offspring2	Rbm46 KO		strain:Rbm46 KO\|isolate:testes\|breed:domescatited strains\|cultivar:the animals were raised in circulating water in southwest university china\|ecotype:the animals were raised in circulating water in southwest university china\|age:4 mpf\|dev stage:adult\|sex:male\|tissue:testes\|BioSampleModel:Model organism or animal									Rbm46 KO	2	2	Testes mRNA profiles of 4 mpf wild type WT and RNA binding protein 46 knockout Rbm46/ zebrafish were generated by deep sequencing mixed sample sequencing using Illumina NextSeq500. The reference genome index was firstly established through Bowtie2 then paired end clean reads were mapped to the zebrafish reference genome using Tophat2 v2.1.0 software according to the standard protocols. Differential expression analysis of control and rbm46 mutant samples was performed using CuffDiff . qRTPCR validation was performed using TaqMan and SYBR Green assays.			RNA-Seq	TRANSCRIPTOMIC	RT-PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP225457			RTm_R1.fq.gz RTm_R2.fq.gz	fastq fastq	6904075800.0	23013586.0	RTm R1.fq.gz	0:150 1:150	A:1611007553;C:1839156029;G:1886442114;T:1567362562;N:107542	150	150			1611007553	1839156029	1886442114	1567362562	107542	SRX6986072	SRS5509254	SRA978539	southwest university\|Key Laboratory of Freshwater Fish Reproduction and	southwest university	2	0.92444	0.92193	0.04174	0.04016	0.67771	0.68308	0.47736	0.47445	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	other	unknown	bulk	unknown	unknown		China	2019-10-14	Adult	Adult	Gonad	Reproductive System