{"database": "metadata", "table": "run_metadata", "rows": [[51110, "SRR8526624", "SRX5329459", "SRS4324035", "SRP183448", "PRJNA520845", "mRNA seq of zebrafish treated with sex hormone 17\u00df 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 17\u00df estradiol E2  CAS: 50 28 2  100 ng/L and masculinized by aromatase inhibitor exemestane EM  CAS: 107868 30 4  10 \u00b5g/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 \u00b5g/L  2 EM + DMSO  3 E2 +DMSO  and 4 EM+ E2 + DMSO.", null, null, null, "E2 64 rep1 [E 64 1]", "GSM3589593", null, "source name:E2 64d whole body|strain:AB|age:64d|treatment:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP", "E2 64 rep1 [E 64 1]", "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 \u201c  dta  x   rna strandness RF\u201d and \u201c  known splicesite infile\u201d 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 \u201c t exon \u2013i gene id  r pos  s reverse\u201d.", "E2 64d whole body", "Zebrafish were treated with EM and/or E2 continuously before sampling for RNA seq. EM and E2 were dissolved in 100 \u03bcg/L DMSO. The treatments included EM 10\u03bcg/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\u2103 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:E2 100ng/L|tissue:whole body|library type:fr firststrand dUTP", "GSM3589593", "GSM3589593: E2 64 rep1 [E 64 1]; Danio rerio; RNA Seq", "GSM3589593", null, "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:GSM3589593", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP183448", null, null, null, null, 4732263300.0, 15774211.0, "GSM3589593 r1", "0:150 1:150", "A:1231004806;C:1113939736;G:1147783646;T:1239495429;N:39683", 150, 150, null, null, 1231004806, 1113939736, 1147783646, 1239495429, 39683, "SRX5329459", "SRS4324035", "SRA843750", "GEO", "College of Life Science and Technology, Huazhong Agricultural University", 2, 0.94551, 0.94929, 0.05467, 0.05373, 0.66728, 0.67083, 0.47358, 0.50808, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-02-04", "Juvenile", "Juvenile", "Trunk", "Surface Structure"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["51110"], "units": {}, "query_ms": 7.72982800117461}