metadata: run_metadata: 16 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation

16 rows where experiment.library_selection = "RANDOM", experiment.platform = "ILLUMINA" and tissue_curation_coarse = "Hematopoietic System"

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.spot_descriptor	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
25142	25142	SRR25649163	SRX21375298	SRS18618391	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.		18843X4	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:spleen\|isolation source:lab cohoused\|replicate:CHM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X4	18843X4	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	18843X4_R1.fastq.gz 18843X4_R2.fastq.gz	fastq fastq	7982656072.0	26432636.0	18843X4 R1.fastq.gz	0:151 1:151	A:2135066517;C:1863182314;G:1988885981;T:1995395692;N:125568	151	151	2135066517	1863182314	1988885981	1995395692	125568	SRX21375298	SRS18618391	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.86144	0.85982	0.30956	0.30838	0.70731	0.71356	0.48481	0.48054	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
25145	25145	SRR25649166	SRX21375295	SRS18618387	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.		18689X9	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:spleen\|isolation source:lab cohoused\|replicate:CHM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X9	18689X9	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	18689X9_R1.fastq.gz 18689X9_R2.fastq.gz	fastq fastq	9420964292.0	31195246.0	18689X9 R1.fastq.gz	0:151 1:151	A:2315675361;C:2390479538;G:2363596017;T:2351024167;N:189209	151	151	2315675361	2390479538	2363596017	2351024167	189209	SRX21375295	SRS18618387	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.87883	0.87875	0.25078	0.24834	0.75394	0.75418	0.60036	0.59504	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
25148	25148	SRR25649169	SRX21375292	SRS18618384	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.		18843X1	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:spleen\|isolation source:lab cohoused\|replicate:CHM1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X1	18843X1	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	18843X1_R1.fastq.gz 18843X1_R2.fastq.gz	fastq fastq	8760175608.0	29007204.0	18843X1 R1.fastq.gz	0:151 1:151	A:2335440655;C:2073187411;G:2210813716;T:2140593603;N:140223	151	151	2335440655	2073187411	2210813716	2140593603	140223	SRX21375292	SRS18618384	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.84641	0.8437	0.21898	0.21841	0.71301	0.72044	0.48661	0.49029	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
25152	25152	SRR25649173	SRX21375288	SRS18618380	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.		18689X11	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:spleen\|isolation source:lab\|replicate:CNTM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X11	18689X11	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	18689X11_R1.fastq.gz 18689X11_R2.fastq.gz	fastq fastq	9515677834.0	31508867.0	18689X11 R1.fastq.gz	0:151 1:151	A:2274021342;C:2477750132;G:2454285243;T:2309429465;N:191652	151	151	2274021342	2477750132	2454285243	2309429465	191652	SRX21375288	SRS18618380	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.87714	0.87737	0.2476	0.24538	0.77968	0.78248	0.63108	0.65333	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
25155	25155	SRR25649176	SRX21375285	SRS18618377	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.		18843X7	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:spleen\|isolation source:lab\|replicate:CNTM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X7	18843X7	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	18843X7_R1.fastq.gz 18843X7_R2.fastq.gz	fastq fastq	9614914732.0	31837466.0	18843X7 R1.fastq.gz	0:151 1:151	A:2577032258;C:2236946505;G:2389573431;T:2411211222;N:151316	151	151	2577032258	2236946505	2389573431	2411211222	151316	SRX21375285	SRS18618377	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.8913	0.88909	0.31019	0.30978	0.71721	0.72557	0.50815	0.52261	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
25158	25158	SRR25649179	SRX21375282	SRS18618374	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.		18689X12	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:spleen\|isolation source:lab\|replicate:CNTF1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X12	18689X12	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	18689X12_R1.fastq.gz 18689X12_R2.fastq.gz	fastq fastq	9338495642.0	30922171.0	18689X12 R1.fastq.gz	0:151 1:151	A:2151902218;C:2516218122;G:2484485366;T:2185704377;N:185559	151	151	2151902218	2516218122	2484485366	2185704377	185559	SRX21375282	SRS18618374	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.88601	0.8889	0.17526	0.17449	0.81702	0.81801	0.46118	0.46609	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Spleen	Hematopoietic System
37103	37103	SRR891512	SRX298192	SRS673882	SRP024369	PRJNA207719	Tissue specific transcriptome profiling of zebrafish	PRJNA207719	Other	Tissue specific transcriptome profiling of zebrafish.		Danio rerio blood	sex:missing\|strain:wild type\|tissue:blood\|health state:normal\|collection date:2013\|geo loc name:India\|biomaterial provider:CSIR Institute of Genomics and Integrative Biology\|age:adult\|BioSampleModel:Model organism or animal	Tissue specific transcriptome of zebrafish	Transcriptome of zebrafish Danio rerio blood	zebrafish blood	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	PAIRED	ILLUMINA	Illumina Genome Analyzer IIx	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP024369	lane6_NoIndex_L006_R2_cat.fastq lane6_NoIndex_L006_R1_cat.fastq	fastq fastq	2122070832.0	20804616.0	Transcriptome of zebrafish Danio rerio blood	0:51 1:51	A:508869849;C:550502747;G:580539251;T:481927903;N:231082	51	51	508869849	550502747	580539251	481927903	231082	SRX298192	SRS673882	SRA089174	CSIR-IGIB	CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology	2	0.78255	0.77496	0.03257	0.03239	0.75672	0.75542	0.44135	0.44382	51	51	B	B	biological fallback assumption	illumina	early_illumina	unknown	random_priming	unknown	bulk	unknown	unknown	India	2013-06-10	Adult	Adult	Blood	Hematopoietic System
41032	41032	SRR3581739	SRX1797279	SRS1465200	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	Larval non fluorescent cells post macrophage sorting3	C NF3	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal	C NF3	C NF3	C NF3	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	C_NF3.fastq.gz	fastq	1745512893.0	34225743.0	C NF3.fastq.gz	0:51	A:470456301;C:396221813;G:401458508;T:477287506;N:88765	51		470456301	396221813	401458508	477287506	88765	SRX1797279	SRS1465200	SRA429046	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.92839		0.06821		0.73099		0.44395		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2016-05-25	Larval	Larval	Blood	Hematopoietic System
41033	41033	SRR3581729	SRX1797278	SRS1465199	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	Larval non fluorescent cells post macrophage sorting2	C NF2	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal	C NF2	C NF2	C NF2	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	C_NF2.fastq.gz	fastq	2116510506.0	41500206.0	C NF2.fastq.gz	0:51	A:580244434;C:475940957;G:474848964;T:585459729;N:16422	51		580244434	475940957	474848964	585459729	16422	SRX1797278	SRS1465199	SRA429045	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.90388		0.06926		0.78963		0.49501		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Larval	Larval	Blood	Hematopoietic System
41034	41034	SRR3581718	SRX1797274	SRS1465196	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	Larval non fluorescent cells post macrophage sorting1	C NF1	breed:*AB\|age:4dpf\|dev stage:Larval\|sex:not determined\|tissue:Whole animal following macrophage depletion via FACS\|BioSampleModel:Model organism or animal	C NF1	C NF1	C NF1	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	C_NF1.fastq.gz	fastq	1492422690.0	29263190.0	C NF1.fastq.gz	0:51	A:421145406;C:327412398;G:328273236;T:415327504;N:264146	51		421145406	327412398	328273236	415327504	264146	SRX1797274	SRS1465196	SRA429041	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.82347		0.08561		0.75207		0.45637		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Larval	Larval	Blood	Hematopoietic System
41038	41038	SRR3581671	SRX1797269	SRS1465191	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	Fluorescence activated cell sorted macrophages1	iRed1	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Fluorescence activated cell sorted macrophages\|BioSampleModel:Model organism or animal	iRed1	iRed1	iRed1	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	iRed1.fastq.gz	fastq	2227229772.0	43671172.0	iRed1.fastq.gz	0:51	A:643185725;C:477251583;G:480258902;T:626515881;N:17681	51		643185725	477251583	480258902	626515881	17681	SRX1797269	SRS1465191	SRA429036	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88005		0.11318		0.76197		0.49474		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41039	41039	SRR3581670	SRX1797268	SRS1465190	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	D rerio dissected M marinum granuloma5	disGran5	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal	disGran5	disGran5	disGran5	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	disGran5.fastq.gz	fastq	2097698850.0	41131350.0	disGran5.fastq.gz	0:51	A:606466942;C:449212134;G:448063993;T:593938942;N:16839	51		606466942	449212134	448063993	593938942	16839	SRX1797268	SRS1465190	SRA429035	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.89212		0.09154		0.76788		0.51096		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41040	41040	SRR3581669	SRX1797267	SRS1465187	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	D rerio dissected M marinum granuloma4	disGran4	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal	disGran4	disGran4	disGran4	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	disGran4.fastq.gz	fastq	2969920485.0	58233735.0	disGran4.fastq.gz	0:51	A:861895830;C:635643178;G:635675729;T:836681349;N:24399	51		861895830	635643178	635675729	836681349	24399	SRX1797267	SRS1465187	SRA429034	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.87215		0.09876		0.7498		0.55116		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41041	41041	SRR3581668	SRX1797266	SRS1465186	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	D rerio dissected M marinum granuloma3	disGran3	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal	disGran3	disGran3	disGran3	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	disGran3.fastq.gz	fastq	2398905207.0	47037357.0	disGran3.fastq.gz	0:51	A:693817641;C:513302774;G:516121702;T:675643798;N:19292	51		693817641	513302774	516121702	675643798	19292	SRX1797266	SRS1465186	SRA429033	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88631		0.10719		0.75465		0.51255		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41042	41042	SRR3581667	SRX1797265	SRS1465185	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	D rerio dissected M marinum granuloma2	disGran2	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal	disGran2	disGran2	disGran2	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	disGran2.fastq.gz	fastq	2108649213.0	41346063.0	disGran2.fastq.gz	0:51	A:606624392;C:457029369;G:459017347;T:585961261;N:16844	51		606624392	457029369	459017347	585961261	16844	SRX1797265	SRS1465185	SRA429032	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.88259		0.10405		0.74282		0.536		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-06-24	Adult	Adult	Blood	Hematopoietic System
41043	41043	SRR3581315	SRX1797076	SRS1465045	SRP075626	PRJNA322629	Mycobacterial infection of adult zebrafish	PRJNA322629	Other	RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.	D rerio dissected M marinum granuloma1	disGran1	breed:*AB\|dev stage:Adult\|sex:pooled male and female\|tissue:Dissected granuloma\|BioSampleModel:Model organism or animal	disGran1	disGran1	disGran1	1	RNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP075626	disGran1.fastq.gz	fastq	2529627234.0	49600534.0	disGran1.fastq.gz	0:51	A:738849065;C:530442613;G:521673896;T:738641232;N:20428	51		738849065	530442613	521673896	738641232	20428	SRX1797076	SRS1465045	SRA428910	Duke University\|Molecular Genetics & Microbiology	Duke University	1	0.81713		0.09754		0.75213		0.51283		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	United States	2017-07-24	Adult	Adult	Blood	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");;