run_metadata: 39626

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
39626	SRR1920170	SRX960486	SRS877483	SRP056356	PRJNA278935	Transcriptome profiling from the brain of male and female zebrafish	GSE67092	Transcriptome Analysis	Genome wide analysis to identify sex specific transcripts in the brain of male and female zebrafish Overall design: Examination of sex specific gene expression in the brain of male vs female zebrafish.				RZB0002 Male	GSM1638734		source name:Male brain tissue\|genotype:Wild type\|Sex:male\|tissue:Brain	RZB0002 Male	Illumina Casava1.8.2 software used for basecalling. Sequenced reads were uniquely mapped to Zv9 genome using tophat v1.4.1. Mapped reads were filtered of reads duplication quality threshold <= 30 and loaded to Genespring NGS Reads per kilobase per megabase RPKM was calculated and normalized using the DeSeq normalization procedure. Genome build: Zv9 Supplementary files format and content: tab delimited text files include Raw RPKM values and normalized RPKM for each Sample.	Male brain tissue		Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.		genotype:Wild type\|Sex:male\|tissue:Brain	GSM1638734	GSM1638734: RZB0002 Male; Danio rerio; RNA Seq	GSM1638734		1	Brain from Male and female fish were extracted for RNA extraction. Brain tissues from 5 fish were collected and pooled. RNA Seq library preparation protocol: Total RNA was extracted using TRIzol® Reagent Invitrogen USA. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. The integrity of RNA samples was determined using an Agilent RNA 6000 Nano chip on an Agilent 2100 Bioanalyzer. Samples with RNA Integrity Number RIN value of 8 9 was used for RNA seq library preparation. Messenger RNA sequencing library was prepared using TruSeq total RNA sample preparation kit Illumina; Total RNA sample preparation guide as per the manufacturers instructions with 3 microgram input RNA per library. Quality of RNA seq library was checked following company recommended protocols. RNA sequencing of male and female samples were performed on the Illumina HiSeq2000 Illumina USA one sample per lane machine with single ended 51 bp read length.	GEO Accession:GSM1638734	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP056356			RZB002_NoIndex_L001_R1_All.fastq.gz	fastq	14711238148.0	193568923.0	GSM1638734 r1	0:76	A:4154125162;C:3219757523;G:3187842434;T:4138123659;N:11389370	76				4154125162	3219757523	3187842434	4138123659	11389370	SRX960486	SRS877483	SRA247878	GEO	Computational and Systems Biology, Genome Institute of Singapore	1	0.91063		0.20427		0.70183		0.50769		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		Singapore	2015-03-20	Undetermined	Undetermined	Brain	Nervous System