metadata: run_metadata: 9 rows where experiment.library_selection = "Oligo-dT", experiment.library_strategy = "RNA-Seq" and tissue

9 rows where experiment.library_selection = "Oligo-dT", experiment.library_strategy = "RNA-Seq" and tissue_curation = "Spleen"

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
71972	71972	SRR22163682	SRX18142568	SRS15644032	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	C3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	C3	C3	control group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	C3.R1.fastq.gz C3.R2.fastq.gz	fastq fastq	6777299176.0	22441388.0	C3.R1.fastq.gz	0:151 1:151	A:1869146927;C:1513142912;G:1565477798;T:1829395893;N:135646	151	151	1869146927	1513142912	1565477798	1829395893	135646	SRX18142568	SRS15644032	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.91581	0.91452	0.09416	0.09344	0.71167	0.71338	0.50247	0.50311	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71973	71973	SRR22163683	SRX18142567	SRS15644031	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	C2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	C2	C2	control group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	C2.R1.fastq.gz C2.R2.fastq.gz	fastq fastq	6956425644.0	23034522.0	C2.R1.fastq.gz	0:151 1:151	A:1847551873;C:1616308106;G:1662475314;T:1829952767;N:137584	151	151	1847551873	1616308106	1662475314	1829952767	137584	SRX18142567	SRS15644031	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93033	0.9312	0.056	0.05619	0.71261	0.71376	0.4668	0.47014	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71974	71974	SRR22163684	SRX18142566	SRS15644030	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	C1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:control\|replicate:replicate1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	C1	C1	control group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	C1.R1.fastq.gz C1.R2.fastq.gz	fastq fastq	6218689172.0	20591686.0	C1.R1.fastq.gz	0:151 1:151	A:1651743119;C:1444992966;G:1490934383;T:1630891482;N:127222	151	151	1651743119	1444992966	1490934383	1630891482	127222	SRX18142566	SRS15644030	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93571	0.93627	0.03427	0.0346	0.73336	0.73401	0.47064	0.47601	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71975	71975	SRR22163685	SRX18142565	SRS15644029	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	B3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	B3	B3	challenge group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	B3.R1.fastq.gz B3.R2.fastq.gz	fastq fastq	7958268062.0	26351881.0	B3.R1.fastq.gz	0:151 1:151	A:2067039750;C:1894612680;G:1943559820;T:2052891379;N:164433	151	151	2067039750	1894612680	1943559820	2052891379	164433	SRX18142565	SRS15644029	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93754	0.93809	0.03309	0.03347	0.71762	0.71731	0.49012	0.4888	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71976	71976	SRR22163686	SRX18142564	SRS15644028	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	B2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	B2	B2	challenge group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	B2.R1.fastq.gz B2.R2.fastq.gz	fastq fastq	7071097158.0	23414229.0	B2.R1.fastq.gz	0:151 1:151	A:1862299896;C:1658740196;G:1713471478;T:1836444697;N:140891	151	151	1862299896	1658740196	1713471478	1836444697	140891	SRX18142564	SRS15644028	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.94335	0.94369	0.04139	0.04172	0.80405	0.80415	0.39649	0.39674	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71977	71977	SRR22163687	SRX18142563	SRS15644027	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	B1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:challenge\|replicate:replicate1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	B1	B1	challenge group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	B1.R1.fastq.gz B1.R2.fastq.gz	fastq fastq	7597788178.0	25158239.0	B1.R1.fastq.gz	0:151 1:151	A:1986638730;C:1797302173;G:1839273564;T:1974418679;N:155032	151	151	1986638730	1797302173	1839273564	1974418679	155032	SRX18142563	SRS15644027	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93891	0.93921	0.04922	0.04888	0.74552	0.74501	0.48725	0.49058	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71978	71978	SRR22163688	SRX18142562	SRS15644026	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	A3	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate3\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	A3	A3	treatment group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	A3.R1.fastq.gz A3.R2.fastq.gz	fastq fastq	8674550152.0	28723676.0	A3.R1.fastq.gz	0:151 1:151	A:2234032232;C:2083164440;G:2128058461;T:2229111717;N:183302	151	151	2234032232	2083164440	2128058461	2229111717	183302	SRX18142562	SRS15644026	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93839	0.93828	0.01889	0.01887	0.73639	0.73724	0.48841	0.47397	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71979	71979	SRR22163689	SRX18142561	SRS15644025	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	A2	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate2\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	A2	A2	treatment group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	A2.R1.fastq.gz A2.R2.fastq.gz	fastq fastq	7383660816.0	24449208.0	A2.R1.fastq.gz	0:151 1:151	A:1917884453;C:1759507724;G:1796259178;T:1909857526;N:151935	151	151	1917884453	1759507724	1796259178	1909857526	151935	SRX18142561	SRS15644025	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93853	0.93854	0.02662	0.02663	0.71435	0.7149	0.49509	0.49212	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic System
71980	71980	SRR22163690	SRX18142560	SRS15644024	SRP405990	PRJNA897077	Transcriptome of zebrafish Danio rerio	PRJNA897077	Other	Zebrafish Danio rerio have been used as a model organism to study innate immune system and hostpathogen interactions. Until now the information related to the immune system against A. hydrophila of zebrafish and the treatment by probiotics is incomplete. To increase knowledge of the molecular mechanisms of the host defense against A. hydrophila and provide evidence that antibiotics can replace by probiotics we conducted transcriptome analysis of spleen in zebrafish 48 h post infection and treatment by Lactococcus lactis post 4h post infection via sequencing.	A1	strain:not applicable\|age:not collected\|sex:not collected\|tissue:spleen\|treatment:treatment\|replicate:replicate1\|BioSampleModel:Model organism or animal	RNA seq of Danio rerio	A1	A1	treatment group	RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP405990	A1.R1.fastq.gz A1.R2.fastq.gz	fastq fastq	7734454352.0	25610776.0	A1.R1.fastq.gz	0:151 1:151	A:2031967267;C:1817027018;G:1866115793;T:2019187811;N:156463	151	151	2031967267	1817027018	1866115793	2019187811	156463	SRX18142560	SRS15644024	SRA1532870	Kunming University of Science and Technology\|Faculty of Life Science and Technology	Kunming University of Science and Technology	2	0.93755	0.93728	0.03692	0.03688	0.71664	0.71693	0.48577	0.48719	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	China	2022-11-02	Undetermined	Undetermined	Spleen	Hematopoietic 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");;