metadata: run_metadata: 6 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "ncRNA-Seq" and tissue

6 rows where experiment.library_layout = "PAIRED", experiment.library_strategy = "ncRNA-Seq" 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

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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");;