run_metadata: 55730

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
55730	SRR10741404	SRX7416888	SRS5863682	SRP238455	PRJNA596870	Transcriptome of juvenile zebrafish treated with the aromatase inhibitor exemestane and solvent control	GSE142353	Transcriptome Analysis	To reveal the transcriptomic changes during the sex differetiation in larval zebrafish we treated the lavarl fish with aromatase inhibitors EM CAS: 107868 30 4 100 µg/L as well as solvent as a control and sampled them post the exposure. Overall design: PolyA+ RNA seq were performed on 6 samples each of which was a mixture of 25 juvenile zebrafish. There are twor groups of larval zebrafish were exposed for two exposure treatments. Each group contained 3 replicates with 25 fish per replicate. The exposure treatments included 1 DMSO 10 µL/L 2 EM + DMSO. The exposure periods were 32 days for zebrafish.	parent bioproject:PRJNA596764	pubmed:31910818		Zebrafish larva EM 32 rep2	GSM4226243		source name:EM 32d replicates2\|tissue:Whole body\|strain:AB\|treatment:EM10μg/L\|age:32d\|library type:fr firststrand dUTP	Zebrafish larva EM 32 rep2	High throughput sequencing raw image data files were converted to reads using fqtools plus analysis. We used FastqC v0.11.8 to evaluate the raw read quality statistics. Reads were mapped to the zebrafish genome Ensembl v95 by Hisat2 v2.0.5 with parameters “ dta x rna strandness RF” and “ known splicesite infile” followed by gene annotation in GTF format Ensembl v95. The output of Hisat2 were converted to BAM format and sorted by Samtools v1.5. 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”.	EM 32d replicates2	The AI EM 6 methylenandrosta 1 4 diene 3 17 dione ≥ 98% purity Bervita used for juvenile zebrafish was dissolved in 10 μg/L DMSO. Two groups of juvenile zebrafish were also raised in continuous exposure to 10 μg/L EM or the solvent control for 32 days.	RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.	Zebrafish AB strain were obtained from China Zebrafish Resource Center and maintained at 28.5 oC with a light/dark cycle of 14/10 h. For each juvenile sample fifty embryos of zebrafish were maintained in a petri dish from 0 dpf and transferred to a three litter tank in the recirculation systems at 5 dpf. They were fed with paramecium at 5 dpf 15 dpf and fairy shrimp at 16 dpf 32 dpf twice a day.	tissue:Whole body\|strain:AB\|treatment:EM10μg/L\|age:32d\|library type:fr firststrand dUTP	GSM4226243	GSM4226243: Zebrafish larva EM 32 rep2; Danio rerio; RNA Seq	GSM4226243		1	RNA samples from each individual were exacted using Trizol Invitrogen according to the manufacturer's protocol. We assessed the overall quality of extracted RNA by GEL RNA purity was checked using the NanoPhotometer spectrophotometer IMPLEN CA USA quantified its concentration with Qubit 3.0 Flurometer Life Technologies CA USA RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the sequencing libraries were prepared at Annoroud Beijing Chinausing VAHTS Stranded mRNA seq Library Prep Kit Vazyme Biotech following the official protocol.	GEO Accession:GSM4226243	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP238455			71_R1.fq 71_R2.fq	fastq fastq	4700869500.0	15669565.0	GSM4226243 r1	0:150 1:150	A:1259665516;C:1078177861;G:1088412868;T:1274486581;N:126674	150	150			1259665516	1078177861	1088412868	1274486581	126674	SRX7416888	SRS5863682	SRA1014473	GEO	College of Life Science and Technology, Huazhong Agricultural University	2	0.93849	0.93427	0.07458	0.07421	0.66214	0.66699	0.51101	0.51068	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		China	2019-12-19	Juvenile	Juvenile	Trunk	Surface Structure