metadata: run_metadata: 27 rows where experiment.library_layout = "PAIRED", experiment.library_source = "METATRANSCRIPTOMIC" and technology = "bulk"

27 rows where experiment.library_layout = "PAIRED", experiment.library_source = "METATRANSCRIPTOMIC" and technology = "bulk"

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
25135	25135	SRR25649156	SRX21375305	SRS18618397	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.	18689X8	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:lab\|replicate:CNTF1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X8	18689X8	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	18689X8_R1.fastq.gz 18689X8_R2.fastq.gz	fastq fastq	8163984120.0	27033060.0	18689X8 R1.fastq.gz	0:151 1:151	A:1900143724;C:2183735704;G:2147710753;T:1932229591;N:164348	151	151	1900143724	2183735704	2147710753	1932229591	164348	SRX21375305	SRS18618397	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.89288	0.89479	0.20193	0.20116	0.79072	0.79352	0.57246	0.56409	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25136	25136	SRR25649157	SRX21375304	SRS18618396	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.	19629X15	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:pet trade 3\|replicate:T3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X15	19629X15	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	19629X15_R2.fastq.gz 19629X15_R1.fastq.gz	fastq fastq	10277997106.0	34033103.0	19629X15 R1.fastq.gz	0:151 1:151	A:2798108841;C:2341310321;G:2438634645;T:2699729301;N:213998	151	151	2798108841	2341310321	2438634645	2699729301	213998	SRX21375304	SRS18618396	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90655	0.90714	0.18082	0.18027	0.72803	0.72953	0.45722	0.45335	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25137	25137	SRR25649158	SRX21375303	SRS18618395	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.	19629X14	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:pet trade 3\|replicate:T2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X14	19629X14	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	19629X14_R1.fastq.gz 19629X14_R2.fastq.gz	fastq fastq	10921707086.0	36164593.0	19629X14 R1.fastq.gz	0:151 1:151	A:2969229092;C:2484790148;G:2595052715;T:2872407360;N:227771	151	151	2969229092	2484790148	2595052715	2872407360	227771	SRX21375303	SRS18618395	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90015	0.90211	0.19548	0.19546	0.72997	0.73131	0.53978	0.54998	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25138	25138	SRR25649159	SRX21375302	SRS18618394	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.	19629X13	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:pet trade 3\|replicate:T1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X13	19629X13	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	19629X13_R1.fastq.gz 19629X13_R2.fastq.gz	fastq fastq	10019262230.0	33176365.0	19629X13 R1.fastq.gz	0:151 1:151	A:2732766602;C:2270429150;G:2391166434;T:2624690350;N:209694	151	151	2732766602	2270429150	2391166434	2624690350	209694	SRX21375302	SRS18618394	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90381	0.90536	0.18425	0.18388	0.72681	0.72936	0.48627	0.49398	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25139	25139	SRR25649160	SRX21375301	SRS18618393	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.	19629X12	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:pet trade 2\|replicate:E3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X12	19629X12	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	19629X12_R1.fastq.gz 19629X12_R2.fastq.gz	fastq fastq	11078632326.0	36684213.0	19629X12 R1.fastq.gz	0:151 1:151	A:2995473302;C:2550446088;G:2653594689;T:2878887522;N:230725	151	151	2995473302	2550446088	2653594689	2878887522	230725	SRX21375301	SRS18618393	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91101	0.91121	0.16145	0.16142	0.70274	0.70498	0.47852	0.48788	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25140	25140	SRR25649161	SRX21375300	SRS18618392	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.	19629X11	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:pet trade 2\|replicate:E2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X11	19629X11	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	19629X11_R1.fastq.gz 19629X11_R2.fastq.gz	fastq fastq	10957183630.0	36282065.0	19629X11 R1.fastq.gz	0:151 1:151	A:2987773085;C:2485587980;G:2603747193;T:2879845340;N:230032	151	151	2987773085	2485587980	2603747193	2879845340	230032	SRX21375300	SRS18618392	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91198	0.91301	0.20992	0.20926	0.73044	0.73316	0.44301	0.43596	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25141	25141	SRR25649162	SRX21375299	SRS18618390	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.	19629X10	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:female\|tissue:intestine\|isolation source:pet trade 2\|replicate:E1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X10	19629X10	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	19629X10_R1.fastq.gz 19629X10_R2.fastq.gz	fastq fastq	9549065142.0	31619421.0	19629X10 R1.fastq.gz	0:151 1:151	A:2603092155;C:2167963952;G:2264536965;T:2513273275;N:198795	151	151	2603092155	2167963952	2264536965	2513273275	198795	SRX21375299	SRS18618390	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.92549	0.92615	0.16176	0.15925	0.7683	0.76926	0.3093	0.30927	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
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
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
25144	25144	SRR25649165	SRX21375296	SRS18618388	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.	18843X6	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:lab cohoused\|replicate:CHM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X6	18843X6	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	18843X6_R1.fastq.gz 18843X6_R2.fastq.gz	fastq fastq	8690806510.0	28777505.0	18843X6 R1.fastq.gz	0:151 1:151	A:2346658651;C:2002583855;G:2108507319;T:2232918222;N:138463	151	151	2346658651	2002583855	2108507319	2232918222	138463	SRX21375296	SRS18618388	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91741	0.91785	0.21796	0.21778	0.6971	0.70102	0.49123	0.51016	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
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
25147	25147	SRR25649168	SRX21375293	SRS18618385	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.	18843X3	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:lab cohoused\|replicate:CHM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X3	18843X3	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	18843X3_R1.fastq.gz 18843X3_R2.fastq.gz	fastq fastq	9351018676.0	30963638.0	18843X3 R1.fastq.gz	0:151 1:151	A:2555870224;C:2133006230;G:2246501165;T:2415491618;N:149439	151	151	2555870224	2133006230	2246501165	2415491618	149439	SRX21375293	SRS18618385	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.91594	0.91512	0.21678	0.21621	0.72719	0.73117	0.52961	0.53327	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
25149	25149	SRR25649170	SRX21375291	SRS18618383	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.	19629X9	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:pet trade 1\|replicate:P3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X9	19629X9	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	19629X9_R1.fastq.gz 19629X9_R2.fastq.gz	fastq fastq	12342730940.0	40869970.0	19629X9 R1.fastq.gz	0:151 1:151	A:3339874828;C:2828928610;G:2945452577;T:3228218292;N:256633	151	151	3339874828	2828928610	2945452577	3228218292	256633	SRX21375291	SRS18618383	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90738	0.8127	0.19825	0.17409	0.73385	0.74659	0.54306	0.55304	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
25151	25151	SRR25649172	SRX21375289	SRS18618381	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.	18689X5	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:lab cohoused\|replicate:CHM1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X5	18689X5	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	18689X5_R1.fastq.gz 18689X5_R2.fastq.gz	fastq fastq	8136028886.0	26940493.0	18689X5 R1.fastq.gz	0:151 1:151	A:2015403368;C:2051480513;G:2023331135;T:2045661742;N:152128	151	151	2015403368	2051480513	2023331135	2045661742	152128	SRX21375289	SRS18618381	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.88067	0.88216	0.24575	0.2425	0.75018	0.75073	0.59361	0.61451	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
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
25154	25154	SRR25649175	SRX21375286	SRS18618378	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.	18843X9	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:lab\|replicate:CNTM3\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18843X9	18843X9	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	18843X9_R1.fastq.gz 18843X9_R2.fastq.gz	fastq fastq	8819654206.0	29204153.0	18843X9 R1.fastq.gz	0:151 1:151	A:2383706177;C:2044504407;G:2140881818;T:2250422256;N:139548	151	151	2383706177	2044504407	2140881818	2250422256	139548	SRX21375286	SRS18618378	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.90385	0.90437	0.21274	0.21235	0.72604	0.73164	0.52888	0.52909	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
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
25157	25157	SRR25649178	SRX21375283	SRS18618375	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.	18689X7	strain:Tubingen\|dev stage:adult\|collection date:2020 11 05\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:lab\|replicate:CNTM2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	18689X7	18689X7	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	18689X7_R1.fastq.gz 18689X7_R2.fastq.gz	fastq fastq	8986035368.0	29755084.0	18689X7 R1.fastq.gz	0:151 1:151	A:2169723143;C:2326462981;G:2292317481;T:2197350043;N:181720	151	151	2169723143	2326462981	2292317481	2197350043	181720	SRX21375283	SRS18618375	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.89254	0.89285	0.22562	0.22356	0.74911	0.75089	0.6409	0.65585	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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
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
25160	25160	SRR25649181	SRX21375280	SRS18618372	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.	19629X8	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:pet trade 1\|replicate:P2\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X8	19629X8	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	19629X8_R2.fastq.gz 19629X8_R1.fastq.gz	fastq fastq	10758135430.0	35622965.0	19629X8 R1.fastq.gz	0:151 1:151	A:2991372806;C:2398155523;G:2517276916;T:2851104238;N:225947	151	151	2991372806	2398155523	2517276916	2851104238	225947	SRX21375280	SRS18618372	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.88839	0.89055	0.23357	0.23344	0.72592	0.72851	0.53343	0.53081	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive System
25161	25161	SRR25649182	SRX21375279	SRS18618371	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.	19629X7	strain:unknown\|dev stage:adult\|collection date:2022 03 15\|geo loc name:USA: Salt Lake City UT\|sex:male\|tissue:intestine\|isolation source:pet trade 1\|replicate:P1\|BioSampleModel:Model organism or animal	RNA seq of adult Danio rerio from laboratory and pet trade sources	19629X7	19629X7	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	19629X7_R1.fastq.gz 19629X7_R2.fastq.gz	fastq fastq	11738178884.0	38868142.0	19629X7 R1.fastq.gz	0:151 1:151	A:3192358555;C:2674045852;G:2784070515;T:3087458659;N:245303	151	151	3192358555	2674045852	2784070515	3087458659	245303	SRX21375279	SRS18618371	SRA1693347	University of Utah\|Quantitative Cell Science	University of Utah	2	0.9074	0.90829	0.20853	0.20916	0.74115	0.74369	0.53704	0.55385	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	random_priming	trueseq	bulk	bulk	bulk	United States	2023-08-15	Adult	Adult	Gut	Digestive 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");;