metadata: run_metadata: 15 rows where devstage_curation = "Multi-stage" and tissue

15 rows where devstage_curation = "Multi-stage" 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.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
68556	68556	SRR18028171	SRX14182301	SRS12005942	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	6WT 3	strain:AB\|isolate:replicate3\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	wt 3 S11 L001 R1	011	011	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz	fastq fastq	3576981600.0	11923272.0	wt 3 S11 L001 R1 001.fastq.gz	0:150 1:150	A:689001630;C:496844981;G:1779990511;T:610974133;N:170345	150	150	689001630	496844981	1779990511	610974133	170345	SRX14182301	SRS12005942	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.8179	0.81697	0.60905	0.60864	0.82692	0.82915	0.52425	0.52623	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68557	68557	SRR18028172	SRX14182300	SRS12005941	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	5WT 2	strain:AB\|isolate:replicate2\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	wt 2 S10 L001 R1	009	009	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz	fastq fastq	4200013800.0	14000046.0	wt 2 S10 L001 R1 001.fastq.gz	0:150 1:150	A:781057232;C:617020885;G:2110010128;T:691723797;N:201758	150	150	781057232	617020885	2110010128	691723797	201758	SRX14182300	SRS12005941	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.8213	0.82216	0.59414	0.59507	0.81089	0.81306	0.53839	0.52755	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68558	68558	SRR18028173	SRX14182299	SRS12005940	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	4WT 1	strain:AB\|isolate:replicate1\|ecotype:wt\|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	wt 1 S9 L001 R1	007	007	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz	fastq fastq	4820063700.0	16066879.0	wt 1 S9 L001 R1 001.fastq.gz	0:150 1:150	A:996304548;C:657334691;G:2379519106;T:786675131;N:230224	150	150	996304548	657334691	2379519106	786675131	230224	SRX14182299	SRS12005940	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.80219	0.80319	0.60906	0.60878	0.83238	0.83303	0.52559	0.51852	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68559	68559	SRR18028174	SRX14182298	SRS12005939	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	3PLD6 3	strain:AB\|isolate:replicate3\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	pld6 3 S3 L003 R1	005	005	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz	fastq fastq	816686700.0	2722289.0	pld6 3 S3 L003 R1 001.fastq.gz	0:150 1:150	A:145681738;C:137123477;G:401610833;T:132256312;N:14340	150	150	145681738	137123477	401610833	132256312	14340	SRX14182298	SRS12005939	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.78314	0.73942	0.07641	0.09097	0.91603	0.91545	0.6312	0.64467	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68560	68560	SRR18028175	SRX14182297	SRS12005938	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	2PLD6 2	strain:AB\|isolate:replicate2\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	pld6 2 S2 L003 R1	003	003	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz	fastq fastq	6546276900.0	21820923.0	pld6 2 S2 L003 R1 001.fastq.gz	0:150 1:150	A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957	150	150	1161502458	1095580994	3226725392	1062358099	109957	SRX14182297	SRS12005938	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.6471	0.593	0.07935	0.09168	0.92058	0.92005	0.53626	0.65284	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68561	68561	SRR18028176	SRX14182296	SRS12005937	SRP359829	PRJNA807002	samll RNA seq of zebrafish gonads of wildtype and pld6 / at 22 dpf	PRJNA807002	Other	In this study we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 / gonad with three repetition. In pld6 / gonad small RNAs mapped to the known piRNA clusters were almost absent. Moreover piRNA clusters in pld6 / gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.	1PLD6 1	strain:AB\|isolate:replicate1\|ecotype:pld6 / \|age:post fertilization day 22\|dev stage:juvenile\|sex:missing\|tissue:Gonad\|BioSampleModel:Model organism or animal	pld6 1 S1 L003 R1	001	001	Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat and three repeats were performed for samll RNA sequencing.	ncRNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	HiSeq X Ten	SRP359829	pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz	fastq fastq	5535130200.0	18450434.0	pld6 1 S1 L003 R1 001.fastq.gz	0:150 1:150	A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680	150	150	1014761790	833992394	2813863824	872418512	93680	SRX14182296	SRS12005937	SRA1372890	Huazhong agricultural university\|School of Life Science and Technology	Huazhong agricultural university	2	0.70358	0.73288	0.08649	0.09366	0.91066	0.90914	0.6197	0.6207	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-02-14	Multi-stage	Multi-stage	Gonad	Reproductive System
68777	68777	SRR18188990	SRX14335888	SRS12150682	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.	GC9	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate3\|BioSampleModel:Model organism or animal	3pgc	3 3pgc	3 3pgc	primordial germ cell from 5 hpf zebrafish embryos	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100	GC9_R1.fq.gz GC9_R2.fq.gz	fastq fastq	16392678600.0	54642262.0	GC9 R1.fq.gz	0:150 1:150	A:4548403510;C:3786937912;G:3801036342;T:4255236177;N:1064659	150	150	4548403510	3786937912	3801036342	4255236177	1064659	SRX14335888	SRS12150682	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.92711	0.93044	0.08622	0.08652	0.79693	0.80306	0.58096	0.58168	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68778	68778	SRR18188991	SRX14335887	SRS12150683	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.	GC4	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate2\|BioSampleModel:Model organism or animal	2pgc	2 2pgc	2 2pgc	primordial germ cell from 5 hpf zebrafish embryos	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100	GC4_R1.fq.gz GC4_R2.fq.gz	fastq fastq	14471348700.0	48237829.0	GC4 R1.fq.gz	0:150 1:150	A:4127039158;C:3211803959;G:3224340004;T:3907215356;N:950223	150	150	4127039158	3211803959	3224340004	3907215356	950223	SRX14335887	SRS12150683	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.91951	0.91886	0.14001	0.14043	0.75777	0.76605	0.55643	0.55313	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68779	68779	SRR18188992	SRX14335886	SRS12150681	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.	GC1	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate1\|BioSampleModel:Model organism or animal	1pgc	1 1pgc	1 1pgc	primordial germ cell from 5 hpf zebrafish embryos	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100	GC1_R1.fq.gz GC1_R2.fq.gz	fastq fastq	18801698100.0	62672327.0	GC1 R1.fq.gz	0:150 1:150	A:5242992703;C:4310290517;G:4334163362;T:4913025193;N:1226325	150	150	5242992703	4310290517	4334163362	4913025193	1226325	SRX14335886	SRS12150681	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.93192	0.93277	0.09532	0.09559	0.78358	0.7906	0.5661	0.56344	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
77261	77261	SRR25434203	SRX21168298	SRS18429832	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	dmrt / 2	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 6\|BioSampleModel:Model organism or animal	RNA seq of gonad	dmrt2	dmrt2	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	dmrt2_R1_.fastq.gz dmrt2_R2.fastq.gz	fastq fastq	5751045000.0	19170150.0	dmrt2 R1 .fastq.gz	0:150 1:150	A:1488645455;C:1371887358;G:1405356847;T:1485112991;N:42349	150	150	1488645455	1371887358	1405356847	1485112991	42349	SRX21168298	SRS18429832	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.91589	0.91745	0.01703	0.01705	0.7637	0.76402	0.47113	0.46945	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	Gonad	Reproductive System
77262	77262	SRR25434204	SRX21168297	SRS18429831	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	dmrt / 1	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 5\|BioSampleModel:Model organism or animal	RNA seq of gonad	dmrt1	dmrt1	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	dmrt1_R2.fastq.gz dmrt1_R1.fastq.gz	fastq fastq	7183531200.0	23945104.0	dmrt1 R1.fastq.gz	0:150 1:150	A:1847909835;C:1724710101;G:1769658622;T:1841199904;N:52738	150	150	1847909835	1724710101	1769658622	1841199904	52738	SRX21168297	SRS18429831	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.92259	0.92339	0.01692	0.01663	0.76558	0.76589	0.46917	0.46678	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	Gonad	Reproductive System
77263	77263	SRR25434205	SRX21168296	SRS18429830	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	cyp17a1 / ;dmrt1 / 2	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 4\|BioSampleModel:Model organism or animal	RNA seq of gonad	dko2	dko2	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	dko2_R2.fastq.gz dko2_R1.fastq.gz	fastq fastq	6765257700.0	22550859.0	dko2 R1.fastq.gz	0:150 1:150	A:1746873541;C:1617601783;G:1668365344;T:1732367309;N:49723	150	150	1746873541	1617601783	1668365344	1732367309	49723	SRX21168296	SRS18429830	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.90858	0.90858	0.02015	0.01977	0.7612	0.76213	0.46791	0.47242	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	Gonad	Reproductive System
77264	77264	SRR25434206	SRX21168295	SRS18429829	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	cyp17a1 / ;dmrt1 / 1	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 3\|BioSampleModel:Model organism or animal	RNA seq of gonad	dko1	dko1	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	dko1_R1.fastq.gz dko1_R2.fastq.gz	fastq fastq	6638354100.0	22127847.0	dko1 R1.fastq.gz	0:150 1:150	A:1713258874;C:1593272953;G:1635070441;T:1696702837;N:48995	150	150	1713258874	1593272953	1635070441	1696702837	48995	SRX21168295	SRS18429829	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.9182	0.91984	0.022	0.02186	0.76118	0.76167	0.47656	0.48847	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	Gonad	Reproductive System
77265	77265	SRR25434207	SRX21168294	SRS18429828	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	Control2	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 2\|BioSampleModel:Model organism or animal	RNA seq of gonad	conf2	conf2	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	conf2_R1.fastq.gz conf2_R2.fastq.gz	fastq fastq	6223727700.0	20745759.0	conf2 R1.fastq.gz	0:150 1:150	A:1590221936;C:1500196214;G:1554765877;T:1578496570;N:47103	150	150	1590221936	1500196214	1554765877	1578496570	47103	SRX21168294	SRS18429828	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.92354	0.92626	0.01495	0.01561	0.76398	0.76418	0.47103	0.46492	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	Gonad	Reproductive System
77266	77266	SRR25434208	SRX21168293	SRS18429827	SRP451673	PRJNA999043	The transcription analysis of gonad in zebrafish	PRJNA999043	Other	To screen out the female biased genes	Control1	isolate:not applicable\|age:80days\|dev stage:Adult\|collection date:2021\|geo loc name:China:Wuhan\|sex:female\|tissue:Gonad\|replicate:replicate = biological replicate 1\|BioSampleModel:Model organism or animal	RNA seq of gonad	conf1	conf1	screen out the key genes	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP451673	conf1_R1.fastq.gz conf1_R2.fastq.gz	fastq fastq	6799767600.0	22665892.0	conf1 R1.fastq.gz	0:150 1:150	A:1740276620;C:1642790185;G:1671812697;T:1744859854;N:28244	150	150	1740276620	1642790185	1671812697	1744859854	28244	SRX21168293	SRS18429827	SRA1681175	Chinese Academy of Sciences\|Institute of Hydrology	Chinese Academy of Sciences	2	0.93305	0.93328	0.01522	0.01517	0.76477	0.76627	0.47519	0.47422	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-07-27	Multi-stage	Multi-stage	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");;