metadata: run_metadata: 20 rows where experiment.library_selection = "RANDOM" and tissue

20 rows where experiment.library_selection = "RANDOM" and tissue_curation = "Kidney"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	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
25143	25143	SRR25649164	SRX21375297	SRS18618389	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18843X5	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:kidney\|isolation source:lab cohoused\|replicate:CHM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X5	18843X5	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18843X5_R1.fastq.gz 18843X5_R2.fastq.gz	fastq fastq	11487744176.0	38038888.0	18843X5 R1.fastq.gz	0:151 1:151	A:3214900282;C:2532228300;G:2651065167;T:3089370892;N:179535	151	151	3214900282	2532228300	2651065167	3089370892	179535	SRX21375297	SRS18618389	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91483	0.91311	0.35213	0.35037	0.68347	0.68826	0.49832	0.49905	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
25146	25146	SRR25649167	SRX21375294	SRS18618386	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18843X2	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:kidney\|isolation source:lab cohoused\|replicate:CHM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X2	18843X2	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18843X2_R2.fastq.gz 18843X2_R1.fastq.gz	fastq fastq	8319888298.0	27549299.0	18843X2 R1.fastq.gz	0:151 1:151	A:2316006657;C:1846379220;G:1965504688;T:2191867233;N:130500	151	151	2316006657	1846379220	1965504688	2191867233	130500	SRX21375294	SRS18618386	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90385	0.90304	0.30055	0.3001	0.68345	0.6901	0.49306	0.48285	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
25150	25150	SRR25649171	SRX21375290	SRS18618382	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18689X1	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:kidney\|isolation source:lab cohoused\|replicate:CHM1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X1	18689X1	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18689X1_R1.fastq.gz 18689X1_R2.fastq.gz	fastq fastq	7723999112.0	25576156.0	18689X1 R1.fastq.gz	0:151 1:151	A:1938376895;C:1923902263;G:1896332244;T:1965229370;N:158340	151	151	1938376895	1923902263	1896332244	1965229370	158340	SRX21375290	SRS18618382	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.87233	0.87262	0.28456	0.28071	0.73858	0.7414	0.60785	0.61428	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
25153	25153	SRR25649174	SRX21375287	SRS18618379	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18843X8	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:kidney\|isolation source:lab\|replicate:CNTM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X8	18843X8	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18843X8_R1.fastq.gz 18843X8_R2.fastq.gz	fastq fastq	7615135964.0	25215682.0	18843X8 R1.fastq.gz	0:151 1:151	A:2157897532;C:1663478819;G:1764954395;T:2028683751;N:121467	151	151	2157897532	1663478819	1764954395	2028683751	121467	SRX21375287	SRS18618379	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91455	0.91333	0.34885	0.34782	0.69467	0.70167	0.50339	0.51371	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
25156	25156	SRR25649177	SRX21375284	SRS18618376	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18689X3	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:kidney\|isolation source:lab\|replicate:CNTM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X3	18689X3	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18689X3_R1.fastq.gz 18689X3_R2.fastq.gz	fastq fastq	8819353112.0	29203156.0	18689X3 R1.fastq.gz	0:151 1:151	A:2342877591;C:2071139579;G:2035896879;T:2369259787;N:179276	151	151	2342877591	2071139579	2035896879	2369259787	179276	SRX21375284	SRS18618376	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.85514	0.85429	0.35095	0.34608	0.72985	0.73077	0.51131	0.53375	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
25159	25159	SRR25649180	SRX21375281	SRS18618373	SRP455253	PRJNA1005695	Metagenomic survey of zebrafish from the laboratory and the pet trade	PRJNA1005695	Other	This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine.		18689X4	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:kidney\|isolation source:lab\|replicate:CNTF1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X4	18689X4	Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample	RNA-Seq	METATRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP455253	18689X4_R1.fastq.gz 18689X4_R2.fastq.gz	fastq fastq	9931670150.0	32886325.0	18689X4 R1.fastq.gz	0:151 1:151	A:2494588549;C:2471174839;G:2445771402;T:2519940959;N:194401	151	151	2494588549	2471174839	2445771402	2519940959	194401	SRX21375281	SRS18618373	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.87391	0.87402	0.31383	0.30879	0.73789	0.74014	0.63365	0.63903	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Kidney	Renal System
51852	51852	SRR10358701	SRX7068102	SRS5584514	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	Model organism or animal sample from Danio rerio	miRNA WT SVCV	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal	miRNA WT SVCV	miRNA WT SVCV	miRNA WT SVCV	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.	miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333	WT-SVCV_1.fastq.gz	fastq	1316699181.0	25817631.0	WT SVCV 1.fastq.gz	0:51	A:276414308;C:338128957;G:380963712;T:321185951;N:6253	51		276414308	338128957	380963712	321185951	6253	SRX7068102	SRS5584514	SRA986546	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.12679		0.0134		0.9931		0.63608		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51853	51853	SRR10358540	SRX7067941	SRS5584353	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	Model organism or animal sample from Danio rerio	miRNA WT Control	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal	miRNA WT Control	miRNA WT Control	miRNA WT Control	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.	miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333	WT-C_1.fastq.gz	fastq	1391330184.0	27280984.0	WT C 1.fastq.gz	0:51	A:252097427;C:365291036;G:426841004;T:347094254;N:6463	51		252097427	365291036	426841004	347094254	6463	SRX7067941	SRS5584353	SRA986495	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.01783		0.00242		0.99411		0.61368		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
63046	63046	SRR13587431	SRX9982126	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	9ZHK	9ZHK	9ZHK	The head kidney experiment repeat 3 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	9ZHK_1.fq.gz 9ZHK_2.fq.gz	fastq fastq	8120179200.0	54134528.0	9ZHK 1.fq.gz	0:150 1:150	A:2233782125;C:1817163304;G:1810150041;T:2259083730;N:0	150	150	2233782125	1817163304	1810150041	2259083730	0	SRX9982126	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.92334		0.08214		0.71926		0.53557		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63047	63047	SRR13587432	SRX9982125	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	24ZHK	24ZHK	24ZHK	The head kidney control repeat 3 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	24ZHK_1.fq.gz 24ZHK_2.fq.gz	fastq fastq	8285296800.0	55235312.0	24ZHK 1.fq.gz	0:150 1:150	A:2319759918;C:1824087204;G:1797861715;T:2343319625;N:268338	150	150	2319759918	1824087204	1797861715	2343319625	268338	SRX9982125	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.93067		0.0988		0.74241		0.55453		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63048	63048	SRR13587433	SRX9982124	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	8ZHK	8ZHK	8ZHK	The head kidney experiment repeat 2 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	8ZHK_1.fq.gz 8ZHK_2.fq.gz	fastq fastq	8153939700.0	54359598.0	8ZHK 1.fq.gz	0:150 1:150	A:2258284333;C:1815761334;G:1799498163;T:2279047560;N:1348310	150	150	2258284333	1815761334	1799498163	2279047560	1348310	SRX9982124	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.91032		0.08827		0.72673		0.51792		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63049	63049	SRR13587434	SRX9982123	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	19Z HK	19Z HK	19Z HK	The head kidney control repeat 2 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	19Z_HK_1.fq.gz 19Z_HK_2.fq.gz	fastq fastq	8406183300.0	56041222.0	19Z HK 1.fq.gz	0:150 1:150	A:2335489974;C:1857072213;G:1842430689;T:2370663226;N:527198	150	150	2335489974	1857072213	1842430689	2370663226	527198	SRX9982123	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.90938		0.09376		0.72486		0.55731		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63050	63050	SRR13587435	SRX9982122	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	10ZHK	10ZHK	10ZHK	The head kidney experiment repeat 1 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	10ZHK_1.fq.gz 10ZHK_2.fq.gz	fastq fastq	8039735100.0	53598234.0	10ZHK 1.fq.gz	0:150 1:150	A:2243931802;C:1770968625;G:1759940752;T:2264893921;N:0	150	150	2243931802	1770968625	1759940752	2264893921	0	SRX9982122	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.9182		0.10087		0.71417		0.54166		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63051	63051	SRR13587436	SRX9982121	SRS8153604	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The head kidney of Danio rerio	isolate:river\|age:adult\|sex:not determined\|tissue:head kidney\|BioSampleModel:Model organism or animal	10Z HK	10Z HK	10Z HK	The head kidney control repeat 1 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	10Z_HK_1.fq.gz 10Z_HK_2.fq.gz	fastq fastq	8419659600.0	56131064.0	10Z HK 1.fq.gz	0:150 1:150	A:2310224890;C:1885764527;G:1880790942;T:2342359008;N:520233	150	150	2310224890	1885764527	1880790942	2342359008	520233	SRX9982121	SRS8153604	SRA1189633	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.91616		0.06612		0.76152		0.37751		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63058	63058	SRR13587413	SRX9982108	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	9ZK	9ZK	9ZK	The kidney experiment repeat 3 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	9ZK_1.fq.gz 9ZK_2.fq.gz	fastq fastq	8175736200.0	54504908.0	9ZK 1.fq.gz	0:150 1:150	A:2263839094;C:1817074671;G:1806345887;T:2288476548;N:0	150	150	2263839094	1817074671	1806345887	2288476548	0	SRX9982108	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.92014		0.08977		0.72236		0.53162		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63059	63059	SRR13587414	SRX9982107	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	24ZK	24ZK	24ZK	The kidney control repeat 3 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	24ZK_1.fq.gz 24ZK_2.fq.gz	fastq fastq	8238567600.0	54923784.0	24ZK 1.fq.gz	0:150 1:150	A:2258633038;C:1860080137;G:1835508827;T:2284016515;N:329083	150	150	2258633038	1860080137	1835508827	2284016515	329083	SRX9982107	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.92468		0.0959		0.70907		0.53327		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63060	63060	SRR13587415	SRX9982106	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	8ZK	8ZK	8ZK	The kidney experiment repeat 2 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	8ZK_1.fq.gz 8ZK_2.fq.gz	fastq fastq	8191887900.0	54612586.0	8ZK 1.fq.gz	0:150 1:150	A:2267646460;C:1825604395;G:1807903598;T:2289958188;N:775259	150	150	2267646460	1825604395	1807903598	2289958188	775259	SRX9982106	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.91157		0.09088		0.72723		0.52217		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63061	63061	SRR13587416	SRX9982105	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	19Z K	19Z K	19Z K	The kidney control repeat 2 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	19Z_K_1.fq.gz 19Z_K_2.fq.gz	fastq fastq	8402134200.0	56014228.0	19Z K 1.fq.gz	0:150 1:150	A:2338499372;C:1849973662;G:1840214821;T:2372961719;N:484626	150	150	2338499372	1849973662	1840214821	2372961719	484626	SRX9982105	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.90113		0.10231		0.72703		0.56124		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63062	63062	SRR13587417	SRX9982104	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	10ZK	10ZK	10ZK	The kidney experiment repeat 1 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	10ZK_1.fq.gz 10ZK_2.fq.gz	fastq fastq	8208016200.0	54720108.0	10ZK 1.fq.gz	0:150 1:150	A:2303193070;C:1796200671;G:1783288010;T:2325334449;N:0	150	150	2303193070	1796200671	1783288010	2325334449	0	SRX9982104	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.9173		0.1039		0.72224		0.541		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal System
63063	63063	SRR13587418	SRX9982103	SRS8153601	SRP303929	PRJNA698005	Danio rerio Raw sequence reads	PRJNA698005	Whole Genome Sequencing	Danio rerio Raw RNA sequence reads	Model organism or animal sample from Danio rerio	The kidney of Danio rerio	isolate:river\|age:adult\|sex:not collected\|tissue:kidney\|BioSampleModel:Model organism or animal	10Z K	10Z K	10Z K	The kidney control repeat 1 of Gobiocypris rarus	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	BGISEQ	BGISEQ-500	SRP303929	10Z_K_1.fq.gz 10Z_K_2.fq.gz	fastq fastq	8205024600.0	54700164.0	10Z K 1.fq.gz	0:150 1:150	A:2259032946;C:1833449876;G:1824313852;T:2287704541;N:523385	150	150	2259032946	1833449876	1824313852	2287704541	523385	SRX9982103	SRS8153601	SRA1189630	Center for Ecological and Environmental Sciences\|Northwestern Polytechnical University	Center for Ecological and Environmental Sciences	1	0.91993		0.0808		0.73308		0.55396		150		B		usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2021-01-30	Adult	Adult	Kidney	Renal 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");;