run_metadata: 40494

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
40494	SRR3204724	SRX1614066	SRS1323928	SRP070923	PRJNA313387	Transcriptomic of ß diketone antibiotics on zebrafish post a 3 month DKAs exposure.	PRJNA313387	Other	RNA libraries were constructed from control 6.25 and 12.5 mg/L treatment groups respectively. post DKAs exposure to 3 mpf zebrafish the whole transcriptome was determined.			12.5 mg/L with equal weight concentrations and volumes for each of the six DKA species ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline was exposure to zebrafish from embryo to 90 dpf dpf	12.5mg/L DKAs	T21		strain:AB strain\|isolate:Oregon State University\|breed:Danio rerio\|cultivar:not applicable\|ecotype:Wild type\|age:3 mpf\|dev stage:3 mpf\|sex:pooled male and female\|tissue:we performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems.\|treatment:12.5 mg/L DKAs exposure\|BioSampleModel:Model organism or animal									12.5mg/L DKAs	T21	1	Zebrafish in 12.5 mg/L β diketone antibiotics treatment groupwith equal weight concentrations and volumes for ofloxacin ciprofloxacin enrofloxacin doxycycline chlortetracycline and oxytetracycline with purity of 99% except for 95% for chlortetracycline were randomly selected post DKAs exposure at 90 dpf and rinsed with phosphorous buffer solution. We performed simple anatomy of the whole fish i.e. removing gill fin and tail tissue while retaining visceral mass head spine and other nerve systems. The retained tissues were used to extract total RNA using Trizol Invitrogen Carlsbad CA USA according to the manufacturer's procedures. The quantity and purity of total RNA were analyzed by employing a Bioanalyzer 2100 and RNA 6000 Nano LabChipKit Agilent Santa Clara CA USA with RIN number >7.0. Poly A mRNA was isolated by poly T oligo attached magnetic beads Invitrogen. The purified mRNA was fragmented into small pieces by divalent cations under elevated temperature. Then the final cDNA library was produced by the reverse transcription of the cleaved RNA fragments on the basis of the mRNA Seq sample preparation kit Illumina San Diego USA and the average 300±50 bp insert size was used for the paired end libraries. Finally the paired end sequencing was performed on an Illumina Hiseq2000/2500. Prior to assembly the low quality reads 1 reads containing sequencing adaptors; 2 reads containing sequencing primer; 3 nucleotide with q scores lower than 20 were removed. Next the cleaned and paired end reads were produced.			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</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>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP070923			T21_Clean_Data1.fq.gz T21_Clean_Data2.fq.gz	fastq fastq	10502615500.0	42010462.0	T21	0:125 1:125	A:2848309151;C:2371408734;G:2356749579;T:2925931092;N:216944	125	125			2848309151	2371408734	2356749579	2925931092	216944	SRX1614066	SRS1323928	SRA359545	School of Life Sciences	School of Life Sciences	2	0.87768	0.88612	0.29688	0.29743	0.68738	0.68363	0.52932	0.52507	125	125	B	B	biological fallback assumption	illumina	hiseq_era	full_length	poly_a	unknown	bulk	unknown	unknown		Unknown	2016-03-16	Adult	Adult	Head	Nervous System