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Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "natural paring late sample", "zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq  replicate1]", "SAMD00073599", null, "sample name:O|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073599", "DRX078023", "zebrafish ovary isolated from adult fish natural paring ovulation. 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Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo maturation inducing hormone DHP treatment", "zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq  replicate1]", "SAMD00073597", null, "sample name:DHP|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073597", "DRX078021", "zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. 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Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo testosterone treatment", "zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq  replicate1]", "SAMD00073596", null, "sample name:TES|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073596", "DRX078020", "zebrafish ovary isolated from adult fish in vivo testosterone treatment. 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Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo diethylstilbestrol DES treatment", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1]", "SAMD00073595", null, "sample name:DES|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073595", "DRX078019", "zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073595", null, null, null, 1532053512.0, 42557042.0, "DRR084188", "0:36", "A:342701220;C:372650449;G:392432461;T:424025702;N:243680", 36, null, null, null, 342701220, 372650449, 392432461, 424025702, 243680, "DRX078019", "DRS086513", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.91276, null, 0.01965, null, 0.77358, null, 0.46461, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [185, "DRR084187", "DRX078018", "DRS086512", "DRP004758", "PRJDB5490", "Fine selection of up regulated genes duirng ovulation by in vivo induction of oocyte maturation and ovulation in zebrafish", "DRP004758", "Other", "Two essential processes  oocyte maturation and ovulation  before oocytes become fertilizable that are independently induced but co operatively proceeded at the final step in oogenesis. Eventhough these two processes are induced by same maturation inducing steroid  17  20 beta dihydroxy 4 pregnen 3 one 17  20 beta DHP  in teleost  the receptor for each pathway is suggested to be different and thus signal transduction pathways are different. While much progresses achieved on the molecular mechanisms for induction of oocyte maturation  the mechanisms to induce ovulation is under elucidation. Previously we established the procedure that can make it possible to prepare the ovarian tissue which contains oocyte maturation induced oocytes in vivo. In the same way  ovulation can be induced in alive zebrafish. Thus it became possible to select the genes up regulated according to ovulation by compare the gene expression between maturation inducing genes in matured oocytes and both maturation and ovulation inducing genes in ovulated eggs. In vivo bioassay has been applied to prepare maturated and ovulated ovarian samples. Specifically up regulated genes to induce ovulation will be selected by RNA seq analysis. The mRNA abundance of highly up regulated genes will be confirmed by q PCR analysis. By this project  ovulation inducing genes will be selected and its roles in induction of ovulation will be addressed in the future.", null, null, "in vivo ethanol treatment", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1]", "SAMD00073594", null, "sample name:EtOH|replicate:biological replicate 1", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00073594", "DRX078018", "zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq  replicate1]", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004758", "Illumina HiSeq 2500 sequencing of SAMD00073594", null, null, null, 1152032724.0, 32000909.0, "DRR084187", "0:36", "A:265166034;C:279617628;G:285136940;T:321928656;N:183466", 36, null, null, null, 265166034, 279617628, 285136940, 321928656, 183466, "DRX078018", "DRS086512", "DRA005484", "SHIZUOKA|Shizuoka University", "Shizuoka University", 1, 0.90791, null, 0.02405, null, 0.75972, null, 0.48931, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2019-01-23", "Adult", "Adult", "Gonad", "Reproductive System"], [40708, "SRR3420428", "SRX1660366", "SRS1360334", "SRP072296", "PRJNA316313", "Codon optimality and mRNA decay in zebrafish and Xenopus", "PRJNA316313", "Other", "Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved \u201ccodon optimality code\u201d that shapes mRNA stability and translation efficiency across vertebrates.", null, null, null, null, "AG01296 testis", null, "strain:TUAB|age:adult|sex:pooled male and female|tissue:Testis|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "AG01296 testis", "AG01296 testis", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP072296", null, null, "AG01296_SEQ0273_R1.fastq.gz", "fastq", 708117840.0, 9317340.0, "AG01296 run 1", "0:76", "A:188728168;C:160744436;G:154540381;T:204071817;N:33038", 76, null, null, null, 188728168, 160744436, 154540381, 204071817, 33038, "SRX1660366", "SRS1360334", "SRA395141", "Yale University|Giraldez Lab", "Yale University", 1, 0.93648, null, 0.13514, null, 0.61302, null, 0.4884, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-17", "Adult", "Adult", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 11, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "PolyA", "p2": "Reproductive System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "TRANSCRIPTOMIC", 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"/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "Adult", "label": "Adult", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System&devstage_curation_coarse=Adult", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "Adult", "label": "Adult", "count": 11, "toggle_url": 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"/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "Gonad", "label": "Gonad", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System&tissue_curation=Gonad", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System", "results": [{"value": "unknown", "label": "unknown", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=PolyA&tissue_curation_coarse=Reproductive+System&technology=unknown", "selected": false}], "truncated": false}}, 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