metadata: run_metadata: 6 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.platform = "DNBSEQ" and tissue

6 rows where experiment.library_source = "TRANSCRIPTOMIC", experiment.platform = "DNBSEQ" and tissue_curation = "Spinal Cord"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	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.study_ref	run.title	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.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
44	44	DRR668250	DRX648352	DRS458865	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 3	Zebrafish 2wpi 3	SAMD00799623	sample name:Zebrafish 2wpi 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 25\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799623	DRX648352	RNA seq of spinal cord in zebrafish at 2wpi injured 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799623	14782516800.0	73912584.0	DRR668250	0:100 1:100	A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943	100	100	4058090278	3335994894	3323563782	4062467903	2399943	DRX648352	DRS458865	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
45	45	DRR668249	DRX648351	DRS458864	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 2	Zebrafish 2wpi 2	SAMD00799622	sample name:Zebrafish 2wpi 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799622	DRX648351	RNA seq of spinal cord in zebrafish at 2wpi injured 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799622	13687641800.0	68438209.0	DRR668249	0:100 1:100	A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902	100	100	3759784620	3087398782	3083881581	3754378915	2197902	DRX648351	DRS458864	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
46	46	DRR668248	DRX648350	DRS458863	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 1	Zebrafish 2wpi 1	SAMD00799621	sample name:Zebrafish 2wpi 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799621	DRX648350	RNA seq of spinal cord in zebrafish at 2wpi injured 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799621	16376197200.0	81880986.0	DRR668248	0:100 1:100	A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189	100	100	4485868844	3700974430	3710833937	4475827800	2692189	DRX648350	DRS458863	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
47	47	DRR668247	DRX648349	DRS458862	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 3	Zebrafish Control 3	SAMD00799620	sample name:Zebrafish Control 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799620	DRX648349	RNA seq of spinal cord in zebrafish at 0wpi control 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799620	13377538600.0	66887693.0	DRR668247	0:100 1:100	A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800	100	100	3725064764	2973653932	2980883214	3695767890	2168800	DRX648349	DRS458862	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
48	48	DRR668246	DRX648348	DRS458861	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 2	Zebrafish Control 2	SAMD00799619	sample name:Zebrafish Control 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799619	DRX648348	RNA seq of spinal cord in zebrafish at 0wpi control 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799619	14971411400.0	74857057.0	DRR668246	0:100 1:100	A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904	100	100	4160326445	3329083037	3329123314	4150453700	2424904	DRX648348	DRS458861	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
49	49	DRR668245	DRX648347	DRS458860	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 1	Zebrafish Control 1	SAMD00799618	sample name:Zebrafish Control 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2024 05 04\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord	DNBSEQ G400 paired end sequencing of SAMD00799618	DRX648347	RNA seq of spinal cord in zebrafish at 0wpi control 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799618	13912523800.0	69562619.0	DRR668245	0:100 1:100	A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776	100	100	3888902049	3079617959	3075111814	3866655202	2236776	DRX648347	DRS458860	DRA020617	Osaka University	Osaka University	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous 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");;