run_metadata: 51124

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
51124	SRR8526610	SRX5329445	SRS4324021	SRP183448	PRJNA520845	mRNA seq of zebrafish treated with sex hormone 17ß estradiol and aromatase inhibitor exemestane during sex development	GSE126039	Transcriptome Analysis	To identify key genes in the early sex development of zebrafish we generated zebrafish AB strain feminized by sex hormone 17ß estradiol E2 CAS: 50 28 2 100 ng/L and masculinized by aromatase inhibitor exemestane EM CAS: 107868 30 4 10 µg/L and detected their transcriptomes by RNA seq. Overall design: PolyA+ RNA seq were performed on 56 samples of four exposure treatments and five exposure periods with 2 3 replicates at each exposure treatment and period. Each sample contained 25 zebrafish. The exposure treatments included 1 DMSO 100 µg/L 2 EM + DMSO 3 E2 +DMSO and 4 EM+ E2 + DMSO.				DMSO 64 rep2 [D 64 2]	GSM3589579		source name:DMSO 64d whole body\|strain:AB\|age:64d\|treatment:DMSO 100μl/L\|tissue:whole body\|library type:fr firststrand dUTP	DMSO 64 rep2 [D 64 2]	High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 and MultiQC v0.9 to evaluate the raw read quality statistics. eads were mapped to the zebrafish genome Ensembl v93 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v93. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. The tool Picard MarkDuplicates v2.18.15 was used to remove duplicates. Genome build: GRCz11 Supplementary files format and content: HTSeq 0.9.1 was used to count reads mapped to each gene with parameters “ t exon –i gene id r pos s reverse”.	DMSO 64d whole body	Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 μg/L DMSO. The treatments included EM 10μg/L and E2 100ng/L either together or alone as well as a solvent control. The water in these groups was refreshed every day with an equivalent concentration of EM E2 and DMSO to ensure the effectiveness of drugs.	We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.	Zebrafish were obtained from Institute of Hydrobiology Chinese Academy of Sciences Wuhan. Embryos were incubated in petri dishes post 0 dpf. Each petri dish contained 50 embryos which were transferred to a three liter tank at 6 dpf. All the zebrafish were maintained at 28.5℃ with a light/dark cycle of 14 hr:10 hr and fed twice daily in tank paramecium at 6 dpf 10 dpf paramecium and fairy shrimp at 11 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf.	strain:AB\|age:64d\|treatment:DMSO 100μl/L\|tissue:whole body\|library type:fr firststrand dUTP	GSM3589579	GSM3589579: DMSO 64 rep2 [D 64 2]; Danio rerio; RNA Seq	GSM3589579		1	We extracted the total RNA using the Trizol method as described in GSE123439. We assessed the overall quality of extracted RNA by GEL measured its purity with NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA and checked its integrity by Agilent 2100 bioanalyzer Agilent Technologies CA USA. Stranded PolyA+ RNA libraries were prepared at Anoroad Beijing China with in house kits. A total of 56 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System Illumina Inc. San Diego CA.	GEO Accession:GSM3589579	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP183448					4455829500.0	14852765.0	GSM3589579 r1	0:150 1:150	A:1201138092;C:1013538556;G:1038336918;T:1202778351;N:37583	150	150			1201138092	1013538556	1038336918	1202778351	37583	SRX5329445	SRS4324021	SRA843750	GEO	College of Life Science and Technology, Huazhong Agricultural University	2	0.93522	0.94269	0.05454	0.05437	0.69053	0.69335	0.56003	0.56129	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		China	2019-02-04	Juvenile	Juvenile	Trunk	Surface Structure