run_metadata: 38359

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
38359	SRR1789379	SRX865976	SRS837148	SRP053202	PRJNA274440	Danio rerio strain:ZF4 cell Transcriptome or Gene expression	PRJNA274440	Other	Zebrafish ZF4 cell exposed to MMS.			zebrafish ZF4 cell post MMS treatment at 24h	MMS	MMS		strain:ZF4\|age:24h\|sex:missing\|tissue:1 dpf zebrafish embryos\|cell line:ZF4\|BioSampleModel:Model organism or animal									The toxicogenomic response of ZF4 cells to methyl methanesulfonate	zebrafish ZF4 cell exposed to MMS	MMS	Library construction: Illumina HiSeq 2000 protocol. Experimental design: MMS Sigma USA was dissolved in phosphate buffered saline PBS just before use. Zebrafish ZF4 cells ATCC CRL 2050 derived from 1 dpf zebrafish embryos were routinely maintained in a humidified chamber 28C 5% CO2 in DMEM/F 12 medium GIBICO USA with 10% v/v fetal bovine serum GIBICO USA 100 U/ml penicillin and 100 mg/ml streptomycin GIBICO USA. When confluence reached 70–80 % cells were treated with 639.16μM MMS or an equal volume of PBS control group and incubated for 24 h. Cells were washed 3 times with cold PBS and detached from the culture plate using trypsin GIBICO USA for further experiments.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>180</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>91</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP053202			MMS_L1_1.fq.gz MMS_L1_2.fq.gz	fastq fastq	4836388500.0	26868825.0	Zebrafish ZF4 cell expoused to MMS	0:90 1:90	A:1311355914;C:1078740323;G:1136692368;T:1309518802;N:81093	90	90			1311355914	1078740323	1136692368	1309518802	81093	SRX865976	SRS837148	SRA236279	Institute of hydrobiology Chinese academy of scie\|Protein Engineering	Institute of hydrobiology Chinese academy of sciences	2	0.93126	0.9293	0.13504	0.13462	0.74008	0.74253	0.55923	0.53956	90	90	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		China	2016-02-04	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures