run_metadata: 39761

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
39761	SRR2127900	SRX1118698	SRS1011435	SRP061587	PRJNA290964	Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos	GSE71346	Transcriptome Analysis	To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.		pubmed:30090366		6 48 control [miRNA seq]	GSM1832840		tissue:embryo control\|strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	6 48 control [miRNA seq]	Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome	embryo control	6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf.	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	zebrafish embryos were selected at 6 hph with normal development.	strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	GSM1832840	GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq	GSM1832840		1	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	GEO Accession:GSM1832840	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP061587			6_48_control.fastq.gz	fastq	308947811.0	6107500.0	GSM1832840 r1	0:50.58 1:0	A:75126425;C:71798677;G:85490341;T:76532368;N:0	50	0			75126425	71798677	85490341	76532368	0	SRX1118698	SRS1011435	SRA280185	GEO	ntu	1	0.00833		0.00166		0.99476		0.42762		51		T		under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown		Unknown	2015-07-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures