metadata: run_metadata: 11 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue

11 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation = "Gonad"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
174	174	DRR084198	DRX078029	DRS086523	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.	in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate2]	SAMD00073605	sample name:TES1 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073605	DRX078029	zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073605			1382763132.0	38410087.0	DRR084198	0:36	A:314367195;C:333340483;G:353519828;T:378654329;N:2881297	36	314367195	333340483	353519828	378654329	2881297	DRX078029	DRS086523	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90366	0.02033	0.77104	0.46543	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
176	176	DRR084196	DRX078027	DRS086521	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.	in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2]	SAMD00073603	sample name:Et 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073603	DRX078027	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073603			1456791660.0	40466435.0	DRR084196	0:36	A:336533534;C:355126203;G:368021063;T:394179246;N:2931614	36	336533534	355126203	368021063	394179246	2931614	DRX078027	DRS086521	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89408	0.02082	0.77027	0.45866	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
177	177	DRR084195	DRX078026	DRS086520	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.	natural paring late sample	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2]	SAMD00073602	sample name:O 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073602	DRX078026	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073602			1627945092.0	45220697.0	DRR084195	0:36	A:381205209;C:392853175;G:410714269;T:439790560;N:3381879	36	381205209	392853175	410714269	439790560	3381879	DRX078026	DRS086520	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.89419	0.02159	0.76848	0.46407	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
178	178	DRR084194	DRX078025	DRS086519	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.	in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate2]	SAMD00073601	sample name:DHP 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073601	DRX078025	zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073601			969680196.0	26935561.0	DRR084194	0:36	A:223558856;C:233793515;G:244712298;T:265549055;N:2066472	36	223558856	233793515	244712298	265549055	2066472	DRX078025	DRS086519	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90178	0.02203	0.76579	0.46491	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
179	179	DRR084193	DRX078024	DRS086518	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.	in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2]	SAMD00073600	sample name:DES 4th\|replicate:biological replicate 2	Illumina HiSeq 2500 sequencing of SAMD00073600	DRX078024	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate2]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073600			825301296.0	22925036.0	DRR084193	0:36	A:189771874;C:198593952;G:209666041;T:225480165;N:1789264	36	189771874	198593952	209666041	225480165	1789264	DRX078024	DRS086518	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90036	0.0197	0.7721	0.45773	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
180	180	DRR084192	DRX078023	DRS086517	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.	natural paring late sample	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1]	SAMD00073599	sample name:O\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073599	DRX078023	zebrafish ovary isolated from adult fish natural paring ovulation. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073599			1474870356.0	40968621.0	DRR084192	0:36	A:334130826;C:361572335;G:369758908;T:409173431;N:234856	36	334130826	361572335	369758908	409173431	234856	DRX078023	DRS086517	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91516	0.02086	0.76792	0.47914	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
182	182	DRR084190	DRX078021	DRS086515	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.	in vivo maturation inducing hormone DHP treatment	zebrafish ovary isolated from adult fish in vivo maturation inducing horm1 DHP treatment. [RNAseq replicate1]	SAMD00073597	sample name:DHP\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073597	DRX078021	zebrafish ovary isolated from adult fish in vivo maturation inducing hormone DHP treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073597			1527194556.0	42422071.0	DRR084190	0:36	A:352068936;C:371030475;G:383086948;T:420761508;N:246689	36	352068936	371030475	383086948	420761508	246689	DRX078021	DRS086515	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91815	0.02248	0.76209	0.46867	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
183	183	DRR084189	DRX078020	DRS086514	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.	in vivo testosterone treatment	zebrafish ovary isolated from adult fish in vivo testoster1 treatment. [RNAseq replicate1]	SAMD00073596	sample name:TES\|replicate:biological replicate 1	Illumina HiSeq 2500 sequencing of SAMD00073596	DRX078020	zebrafish ovary isolated from adult fish in vivo testosterone treatment. [RNAseq replicate1]	1	Agilent SureSelect Strand Specific RNA Prep Kit	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 SAMD00073596			1403618796.0	38989411.0	DRR084189	0:36	A:321063874;C:342718133;G:352434647;T:387171455;N:230687	36	321063874	342718133	352434647	387171455	230687	DRX078020	DRS086514	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91583	0.02212	0.76073	0.47596	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
184	184	DRR084188	DRX078019	DRS086513	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.	in vivo diethylstilbestrol DES treatment	zebrafish ovary isolated from adult fish in vivo diethylstilbestrol DES treatment. [RNAseq replicate1]	SAMD00073595	sample name:DES\|replicate:biological replicate 1	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	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			1532053512.0	42557042.0	DRR084188	0:36	A:342701220;C:372650449;G:392432461;T:424025702;N:243680	36	342701220	372650449	392432461	424025702	243680	DRX078019	DRS086513	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.91276	0.01965	0.77358	0.46461	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
185	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.	in vivo ethanol treatment	zebrafish ovary isolated from adult fish in vivo ethanol treatment. [RNAseq replicate1]	SAMD00073594	sample name:EtOH\|replicate:biological replicate 1	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	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			1152032724.0	32000909.0	DRR084187	0:36	A:265166034;C:279617628;G:285136940;T:321928656;N:183466	36	265166034	279617628	285136940	321928656	183466	DRX078018	DRS086512	DRA005484	SHIZUOKA\|Shizuoka University	Shizuoka University	1	0.90791	0.02405	0.75972	0.48931	36	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Japan	2019-01-23	Adult	Adult	Gonad	Reproductive System
40708	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 “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.			AG01296 testis	strain:TUAB\|age:adult\|sex:pooled male and female\|tissue:Testis\|BioSampleModel:Model organism or animal	AG01296 testis	AG01296 testis	1	1		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		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	188728168	160744436	154540381	204071817	33038	SRX1660366	SRS1360334	SRA395141	Yale University\|Giraldez Lab	Yale University	1	0.93648	0.13514	0.61302	0.4884	76	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	United States	2016-06-17	Adult	Adult	Gonad	Reproductive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;