metadata: run_metadata: 86 rows where experiment.library

86 rows where experiment.library_source = "METATRANSCRIPTOMIC"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	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
14	14	DRR334977	DRX323973	DRS217313	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 3	SAMD00422597	sample name:rRNA mock community 28 degrees rep 3\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422597	DRX323973	t28 3 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422597			3791170746.0	37701921.0	DRR334977	0:100.56 1:0	A:967477491;C:926887571;G:898697642;T:998107868;N:174	100	0	967477491	926887571	898697642	998107868	174	DRX323973	DRS217313	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.31527		0.06446		0.88844		0.62118		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
15	15	DRR334976	DRX323972	DRS217312	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 2	SAMD00422596	sample name:rRNA mock community 28 degrees rep 2\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422596	DRX323972	t28 2 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422596			2801693695.0	27860658.0	DRR334976	0:100.56 1:0	A:700189496;C:702936549;G:679920984;T:718646067;N:599	100	0	700189496	702936549	679920984	718646067	599	DRX323972	DRS217312	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.43508		0.08819		0.85859		0.69447		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
16	16	DRR334975	DRX323971	DRS217311	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 28 degrees rep 1	SAMD00422595	sample name:rRNA mock community 28 degrees rep 1\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:28\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422595	DRX323971	t28 1 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422595			3148691934.0	31307464.0	DRR334975	0:100.57 1:0	A:785000734;C:791315678;G:766594599;T:805780465;N:458	100	0	785000734	791315678	766594599	805780465	458	DRX323971	DRS217311	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.37139		0.09061		0.94065		0.74047		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
17	17	DRR334974	DRX323970	DRS217310	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 3	SAMD00422594	sample name:rRNA mock community 19 degrees rep 3\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422594	DRX323970	t19 3 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422594			2856186273.0	28400524.0	DRR334974	0:100.57 1:0	A:695685787;C:733754277;G:715270279;T:711475544;N:386	100	0	695685787	733754277	715270279	711475544	386	DRX323970	DRS217310	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.48152		0.10933		0.87105		0.7287		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
18	18	DRR334973	DRX323969	DRS217309	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 2	SAMD00422593	sample name:rRNA mock community 19 degrees rep 2\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422593	DRX323969	t19 2 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422593			3199929804.0	31816971.0	DRR334973	0:100.57 1:0	A:777149590;C:825478743;G:804835148;T:792466124;N:199	100	0	777149590	825478743	804835148	792466124	199	DRX323969	DRS217309	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.4418		0.10282		0.89706		0.74667		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
19	19	DRR334972	DRX323968	DRS217308	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 19 degrees rep 1	SAMD00422592	sample name:rRNA mock community 19 degrees rep 1\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:19\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422592	DRX323968	t19 1 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422592			3658675391.0	36374718.0	DRR334972	0:100.58 1:0	A:879342063;C:954687406;G:929537615;T:895107890;N:417	100	0	879342063	954687406	929537615	895107890	417	DRX323968	DRS217308	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.49439		0.11691		0.88239		0.73925		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
20	20	DRR334971	DRX323967	DRS217307	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 3	SAMD00422591	sample name:rRNA mock community 10 degrees rep 3\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422591	DRX323967	t10 3 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422591			3017524690.0	30006334.0	DRR334971	0:100.56 1:0	A:771967717;C:738814269;G:712866126;T:793876235;N:343	100	0	771967717	738814269	712866126	793876235	343	DRX323967	DRS217307	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.33157		0.07363		0.9093		0.73422		100		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
21	21	DRR334970	DRX323966	DRS217306	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 2	SAMD00422590	sample name:rRNA mock community 10 degrees rep 2\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422590	DRX323966	t10 2 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422590			3115915184.0	30982336.0	DRR334970	0:100.57 1:0	A:765727966;C:794741415;G:771082024;T:784363609;N:170	100	0	765727966	794741415	771082024	784363609	170	DRX323966	DRS217306	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.45458		0.10504		0.89357		0.749		100		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
22	22	DRR334969	DRX323965	DRS217305	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	totalRNA metatranscriptomic sequences from mock communities consist of five model species	rRNA mock community at 10 degrees rep 1	SAMD00422589	sample name:rRNA mock community 10 degrees rep 1\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:10\|treatment:rRNA	NextSeq 2000 sequencing of SAMD00422589	DRX323965	t10 1 tRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422589			3206657309.0	31883532.0	DRR334969	0:100.57 1:0	A:792874386;C:814578518;G:787469614;T:811734581;N:210	100	0	792874386	814578518	787469614	811734581	210	DRX323965	DRS217305	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.40156		0.09664		0.92898		0.74114		101		B		usable mapping rate	illumina	nextseq_v2	unknown	random_priming	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
23	23	DRR334968	DRX323964	DRS217304	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 3	SAMD00422588	sample name:mRNA mock community 28 degrees rep 3\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422588	DRX323964	m28 3 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422588			3157078356.0	31416275.0	DRR334968	0:100.49 1:0	A:816263259;C:752748024;G:759884392;T:828182261;N:420	100	0	816263259	752748024	759884392	828182261	420	DRX323964	DRS217304	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.64888		0.01832		0.73996		0.46811		99		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
24	24	DRR334967	DRX323963	DRS217303	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 2	SAMD00422587	sample name:mRNA mock community 28 degrees rep 2\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422587	DRX323963	m28 2 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422587			3155807651.0	31404635.0	DRR334967	0:100.49 1:0	A:819014350;C:749873295;G:756284406;T:830635394;N:206	100	0	819014350	749873295	756284406	830635394	206	DRX323963	DRS217303	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.76742		0.02238		0.72427		0.47376		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
25	25	DRR334966	DRX323962	DRS217302	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 28 degrees rep 1	SAMD00422586	sample name:mRNA mock community 28 degrees rep 1\|biological replicate:3\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:28\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422586	DRX323962	m28 1 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422586			2589772286.0	25765782.0	DRR334966	0:100.51 1:0	A:679223577;C:610675892;G:617869465;T:682003195;N:157	100	0	679223577	610675892	617869465	682003195	157	DRX323962	DRS217302	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.42984		0.03367		0.73555		0.49223		100		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
26	26	DRR334965	DRX323961	DRS217318	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 3	SAMD00422602	sample name:mRNA mock community 19 degrees rep 3\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422602	DRX323961	m19 3 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422602			3124746628.0	31095367.0	DRR334965	0:100.49 1:0	A:821891547;C:734660854;G:739230475;T:828963220;N:532	100	0	821891547	734660854	739230475	828963220	532	DRX323961	DRS217318	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.72881		0.03264		0.69449		0.47416		99		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
27	27	DRR334964	DRX323960	DRS217317	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 2	SAMD00422601	sample name:mRNA mock community 19 degrees rep 2\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422601	DRX323960	m19 2 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422601			3171661466.0	31561473.0	DRR334964	0:100.49 1:0	A:836793307;C:742872021;G:750053514;T:841942389;N:235	100	0	836793307	742872021	750053514	841942389	235	DRX323960	DRS217317	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.63153		0.03639		0.69027		0.48494		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
28	28	DRR334963	DRX323959	DRS217316	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 19 degrees rep 1	SAMD00422600	sample name:mRNA mock community 19 degrees rep 1\|biological replicate:2\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:19\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422600	DRX323959	m19 1 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422600			2916453082.0	29023768.0	DRR334963	0:100.48 1:0	A:761416880;C:692014182;G:696272089;T:766749729;N:202	100	0	761416880	692014182	696272089	766749729	202	DRX323959	DRS217316	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.71651		0.03406		0.68696		0.47496		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
29	29	DRR334962	DRX323958	DRS217315	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 3	SAMD00422599	sample name:mRNA mock community 10 degrees rep 3\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:3\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422599	DRX323958	m10 3 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422599			2600103192.0	25872833.0	DRR334962	0:100.50 1:0	A:668944597;C:625686885;G:631010166;T:674461210;N:334	100	0	668944597	625686885	631010166	674461210	334	DRX323958	DRS217315	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.57077		0.02949		0.71918		0.47633		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
30	30	DRR334961	DRX323957	DRS217314	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 2	SAMD00422598	sample name:mRNA mock community 10 degrees rep 2\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:2\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422598	DRX323957	m10 2 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422598			2608660833.0	25958804.0	DRR334961	0:100.49 1:0	A:683370128;C:615324906;G:621209484;T:688756167;N:148	100	0	683370128	615324906	621209484	688756167	148	DRX323957	DRS217314	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.63764		0.04316		0.69656		0.48579		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
31	31	DRR334960	DRX323956	DRS217301	DRP008001	PRJDB12578	Allometric scaling of RNA abundance from genes to communities	DRP008001	Other	The metabolic theory of ecology MTE and growth rate hypothesis GRH help explain the mechanistic basis of size allometry and temperature dependence on growth rate and whole body RNA content in organisms. However testing RNA allometric scaling with next generation sequencing is yet to be done. Here we validated the assumptions of GRH and MTE on messenger RNA and ribosome abundance using mock community metatranscriptome analysis. Our findings highlight that fast growing smaller species harbor greater RNA abundance per mass of tissue compared with species having larger body sizes and slower growth rates. We found that genome size and body size impose significant constraints in interspecific RNA abundance scaling while the assumed temperature dependence appeared to be weak. Lastly allometric scaling integration in community level models may extend the use of metatranscriptomics as a reliable tool for estimating ecosystem processes.	mRNA metatranscriptomic sequences from mock communities consist of five model species	mRNA mock community at 10 degrees rep 1	SAMD00422585	sample name:mRNA mock community 10 degrees rep 1\|biological replicate:1\|collection date:2021 01 15\|dev stage:Adult\|technical replicate:1\|temp:10\|treatment:mRNA	NextSeq 2000 sequencing of SAMD00422585	DRX323956	m10 1 mRNA.fastq	1	NEBNext Kit for Illumina	RNA-Seq	METATRANSCRIPTOMIC	PolyA	SINGLE	ILLUMINA	NextSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	DRP008001	NextSeq 2000 sequencing of SAMD00422585			2879915507.0	28651533.0	DRR334960	0:100.52 1:0	A:761972464;C:675761096;G:678969165;T:763212637;N:145	100	0	761972464	675761096	678969165	763212637	145	DRX323956	DRS217301	DRA013226	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	SINICA\|Machida Laboratory Biodiversity Research Center, Academia Sinica	1	0.47851		0.05671		0.72622		0.49269		101		B		usable mapping rate	illumina	nextseq_v2	unknown	poly_a	nebnext	bulk	unknown	unknown	Taiwan	2021-12-23	Adult	Adult	Undetermined	Undetermined
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
30650	30650	SRR28054745	SRX23704460	SRS20534455	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1228	library ID:H 1\|title:High 1\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1228 rep1 1 URNA S72 L003 R1 001.fastq\|filename2:S21K1228 rep1 1 URNA S72 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	High 1	H 1	H 1	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1228_rep1_1_URNA_S72_L003_R1_001.fastq.gz S21K1228_rep1_1_URNA_S72_L003_R2_001.fastq.gz	fastq fastq	6506930400.0	21689768.0	S21K1228 rep1 1 URNA S72 L003 R1 001.fastq.gz	0:150 1:150	A:1750770382;C:1473474222;G:1551729505;T:1730941027;N:15264	150	150	1750770382	1473474222	1551729505	1730941027	15264	SRX23704460	SRS20534455	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30651	30651	SRR28054746	SRX23704459	SRS20534452	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1227	library ID:M 3\|title:Medium 3\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1227 rep1 1 URNA S71 L003 R1 001.fastq\|filename2:S21K1227 rep1 1 URNA S71 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Medium 3	M 3	M 3	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1227_rep1_1_URNA_S71_L003_R1_001.fastq.gz S21K1227_rep1_1_URNA_S71_L003_R2_001.fastq.gz	fastq fastq	6899268300.0	22997561.0	S21K1227 rep1 1 URNA S71 L003 R1 001.fastq.gz	0:150 1:150	A:1858425383;C:1565856426;G:1639602501;T:1835367744;N:16246	150	150	1858425383	1565856426	1639602501	1835367744	16246	SRX23704459	SRS20534452	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30652	30652	SRR28054747	SRX23704458	SRS20534453	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1226	library ID:M 2\|title:Medium 2\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1226 rep1 1 URNA S70 L003 R1 001.fastq\|filename2:S21K1226 rep1 1 URNA S70 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Medium 2	M 2	M 2	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1226_rep1_1_URNA_S70_L003_R1_001.fastq.gz S21K1226_rep1_1_URNA_S70_L003_R2_001.fastq.gz	fastq fastq	6310969500.0	21036565.0	S21K1226 rep1 1 URNA S70 L003 R1 001.fastq.gz	0:150 1:150	A:1688391347;C:1451351943;G:1503321023;T:1667755412;N:149775	150	150	1688391347	1451351943	1503321023	1667755412	149775	SRX23704458	SRS20534453	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30653	30653	SRR28054748	SRX23704457	SRS20534454	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1225	library ID:M 1\|title:Medium 1\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1225 rep1 1 URNA S69 L003 R1 001.fastq\|filename2:S21K1225 rep1 1 URNA S69 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Medium 1	M 1	M 1	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1225_rep1_1_URNA_S69_L003_R1_001.fastq.gz S21K1225_rep1_1_URNA_S69_L003_R2_001.fastq.gz	fastq fastq	8677007700.0	28923359.0	S21K1225 rep1 1 URNA S69 L003 R1 001.fastq.gz	0:150 1:150	A:2318840740;C:1999375306;G:2068690840;T:2290080340;N:20474	150	150	2318840740	1999375306	2068690840	2290080340	20474	SRX23704457	SRS20534454	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30654	30654	SRR28054749	SRX23704456	SRS20534450	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1224	library ID:L 3\|title:Low 3\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1224 rep1 1 URNA S68 L003 R1 001.fastq\|filename2:S21K1224 rep1 1 URNA S68 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Low 3	L 3	L 3	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1224_rep1_1_URNA_S68_L003_R1_001.fastq.gz S21K1224_rep1_1_URNA_S68_L003_R2_001.fastq.gz	fastq fastq	7160279400.0	23867598.0	S21K1224 rep1 1 URNA S68 L003 R1 001.fastq.gz	0:150 1:150	A:1893984011;C:1641393143;G:1753657602;T:1871228004;N:16640	150	150	1893984011	1641393143	1753657602	1871228004	16640	SRX23704456	SRS20534450	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30655	30655	SRR28054750	SRX23704455	SRS20534451	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1223	library ID:L 2\|title:Low 2\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1223 rep1 1 URNA S67 L003 R1 001.fastq\|filename2:S21K1223 rep1 1 URNA S67 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Low 2	L 2	L 2	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1223_rep1_1_URNA_S67_L003_R1_001.fastq.gz S21K1223_rep1_1_URNA_S67_L003_R2_001.fastq.gz	fastq fastq	6779124000.0	22597080.0	S21K1223 rep1 1 URNA S67 L003 R1 001.fastq.gz	0:150 1:150	A:1804338053;C:1556291420;G:1636850001;T:1781628665;N:15861	150	150	1804338053	1556291420	1636850001	1781628665	15861	SRX23704455	SRS20534451	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30656	30656	SRR28054751	SRX23704454	SRS20534449	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1222	library ID:L 1\|title:Low 1\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1222 rep1 1 URNA S66 L003 R1 001.fastq\|filename2:S21K1222 rep1 1 URNA S66 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Low 1	L 1	L 1	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1222_rep1_1_URNA_S66_L003_R1_001.fastq.gz S21K1222_rep1_1_URNA_S66_L003_R2_001.fastq.gz	fastq fastq	7484014500.0	24946715.0	S21K1222 rep1 1 URNA S66 L003 R1 001.fastq.gz	0:150 1:150	A:1895991723;C:1633895559;G:2095064183;T:1859045639;N:17396	150	150	1895991723	1633895559	2095064183	1859045639	17396	SRX23704454	SRS20534449	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30657	30657	SRR28054752	SRX23704453	SRS20534447	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1221	library ID:C 3\|title:Control 3\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1221 rep1 1 URNA S65 L003 R1 001.fastq\|filename2:S21K1221 rep1 1 URNA S65 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Control 3	C 3	C 3	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1221_rep1_1_URNA_S65_L003_R1_001.fastq.gz S21K1221_rep1_1_URNA_S65_L003_R2_001.fastq.gz	fastq fastq	6562506000.0	21875020.0	S21K1221 rep1 1 URNA S65 L003 R1 001.fastq.gz	0:150 1:150	A:1753018331;C:1507753283;G:1569109292;T:1732610076;N:15018	150	150	1753018331	1507753283	1569109292	1732610076	15018	SRX23704453	SRS20534447	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30658	30658	SRR28054753	SRX23704452	SRS20534448	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1230	library ID:H 3\|title:High 3\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq\|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	High 3	H 3	H 3	missing		RNA-Seq	METATRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz	fastq fastq	6117817800.0	20392726.0	S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz	0:150 1:150	A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211	150	150	1635728688	1405168032	1464072107	1612834762	14211	SRX23704452	SRS20534448	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30659	30659	SRR28054754	SRX23704451	SRS20534446	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1229	library ID:H 2\|title:High 2\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1229 rep1 1 URNA S73 L003 R1 001.fastq\|filename2:S21K1229 rep1 1 URNA S73 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	High 2	H 2	H 2	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1229_rep1_1_URNA_S73_L003_R1_001.fastq.gz S21K1229_rep1_1_URNA_S73_L003_R2_001.fastq.gz	fastq fastq	7164803100.0	23882677.0	S21K1229 rep1 1 URNA S73 L003 R1 001.fastq.gz	0:150 1:150	A:1920286881;C:1649856655;G:1697032084;T:1897610671;N:16809	150	150	1920286881	1649856655	1697032084	1897610671	16809	SRX23704451	SRS20534446	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30660	30660	SRR28054755	SRX23704450	SRS20534445	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1220	library ID:C 2\|title:Control 2\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1220 rep1 1 URNA S64 L003 R1 001.fastq\|filename2:S21K1220 rep1 1 URNA S64 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Control 2	C 2	C 2	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1220_rep1_1_URNA_S64_L003_R1_001.fastq.gz S21K1220_rep1_1_URNA_S64_L003_R2_001.fastq.gz	fastq fastq	6790504800.0	22635016.0	S21K1220 rep1 1 URNA S64 L003 R1 001.fastq.gz	0:150 1:150	A:1784553430;C:1593393319;G:1650087761;T:1762454671;N:15619	150	150	1784553430	1593393319	1650087761	1762454671	15619	SRX23704450	SRS20534445	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
30661	30661	SRR28054756	SRX23704449	SRS20534444	SRP491086	PRJNA1078753	Integrated mRNA and miRNA sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos	PRJNA1078753	Other	Tobacco pollutants are prevalent in the environment leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore in this study we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25% 1% and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity including increased mortality and decreased incubation rate in a dose dependent manner. Moreover CSE induced malformations and apoptosis specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment apoptosis disorder and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.			S21K1219	library ID:C 1\|title:Control 1\|library strategy:OTHER\|library source:METATRANSCRIPTIOMIC\|library selection:other\|library layout:paired\|platform:ILLUMINA\|instrument model:RNA seq\|filetype:fastq\|filename:S21K1219 rep1 1 URNA S63 L003 R1 001.fastq\|filename2:S21K1219 rep1 1 URNA S63 L003 R2 001.fastq\|host:missing\|isolation source:missing\|collection date:missing\|geographic location:missing\|latitude and longitude:missing\|age:missing\|breed:missing\|cultivar:missing\|dev stage:missing\|ecotype:missing\|isolate:missing\|sex:missing\|strain:missing\|tissue:missing\|BioSampleModel:Model organism or animal	Control 1	C 1	C 1	missing		RNA-Seq	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP491086		S21K1219_rep1_1_URNA_S63_L003_R1_001.fastq.gz S21K1219_rep1_1_URNA_S63_L003_R2_001.fastq.gz	fastq fastq	7498264200.0	24994214.0	S21K1219 rep1 1 URNA S63 L003 R1 001.fastq.gz	0:150 1:150	A:2002773492;C:1716996682;G:1800329295;T:1978147319;N:17412	150	150	2002773492	1716996682	1800329295	1978147319	17412	SRX23704449	SRS20534444	SRA1806456	The Second Affiliated Hospital of Shantou University Medical College\|Department of Burns and Plastic Surgery	The Second Affiliated Hospital of Shantou University Medical College												B	B	biological fallback assumption	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2024-02-22	Undetermined	Multi-stage	Undetermined	Undetermined
32508	32508	SRR29290248	SRX24807391	SRS21522263	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 1	liver transcriptome	L4 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L4 1	L4 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMFA6-7L.R1.fq.gz TMFA6-7L.R2.fq.gz	fastq fastq	5892231600.0	19640772.0	TMFA6 7L.R1.fq.gz	0:150 1:150	A:1471743634;C:1450664701;G:1502453832;T:1466956960;N:412473	150	150	1471743634	1450664701	1502453832	1466956960	412473	SRX24807391	SRS21522263	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32509	32509	SRR29290249	SRX24807390	SRS21522262	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 3	liver transcriptome	L3 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L3 3	L3 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLSC-5L.R1.fq.gz TLSC-5L.R2.fq.gz	fastq fastq	6269295000.0	20897650.0	TLSC 5L.R1.fq.gz	0:150 1:150	A:1541736942;C:1578334203;G:1620160556;T:1528907120;N:156179	150	150	1541736942	1578334203	1620160556	1528907120	156179	SRX24807390	SRS21522262	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32510	32510	SRR29290250	SRX24807389	SRS21522261	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 2	liver transcriptome	L3 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L3 2	L3 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLSB-3L.R1.fq.gz TLSB-3L.R2.fq.gz	fastq fastq	6206673000.0	20688910.0	TLSB 3L.R1.fq.gz	0:150 1:150	A:1592564670;C:1487253074;G:1531600191;T:1595004475;N:250590	150	150	1592564670	1487253074	1531600191	1595004475	250590	SRX24807389	SRS21522261	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32511	32511	SRR29290251	SRX24807388	SRS21522260	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 1	liver transcriptome	L3 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 23\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L3 1	L3 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLSA-1L.R1.fq.gz TLSA-1L.R2.fq.gz	fastq fastq	6188928300.0	20629761.0	TLSA 1L.R1.fq.gz	0:150 1:150	A:1584479312;C:1464260894;G:1549296685;T:1590644766;N:246643	150	150	1584479312	1464260894	1549296685	1590644766	246643	SRX24807388	SRS21522260	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32512	32512	SRR29290252	SRX24807387	SRS21522259	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 3	liver transcriptome	L2 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L2 3	L2 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLFC1-3L.R1.fq.gz TLFC1-3L.R2.fq.gz	fastq fastq	6367070400.0	21223568.0	TLFC1 3L.R1.fq.gz	0:150 1:150	A:1579430230;C:1587605262;G:1613210542;T:1586578782;N:245584	150	150	1579430230	1587605262	1613210542	1586578782	245584	SRX24807387	SRS21522259	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32513	32513	SRR29290253	SRX24807386	SRS21522258	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 2	liver transcriptome	L2 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L2 2	L2 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLFB1-3L.R1.fq.gz TLFB1-3L.R2.fq.gz	fastq fastq	6996653100.0	23322177.0	TLFB1 3L.R1.fq.gz	0:150 1:150	A:1803878205;C:1678057588;G:1715367000;T:1799170285;N:180022	150	150	1803878205	1678057588	1715367000	1799170285	180022	SRX24807386	SRS21522258	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32514	32514	SRR29290254	SRX24807385	SRS21522257	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 1	liver transcriptome	L2 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 08\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposed to 120 or above tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L2 1	L2 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TLFA6-7L.R1.fq.gz TLFA6-7L.R2.fq.gz	fastq fastq	6109509300.0	20365031.0	TLFA6 7L.R1.fq.gz	0:150 1:150	A:1525902154;C:1507317327;G:1549698641;T:1526193716;N:397462	150	150	1525902154	1507317327	1549698641	1526193716	397462	SRX24807385	SRS21522257	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32515	32515	SRR29290255	SRX24807384	SRS21522256	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 3	liver transcriptome	L7 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L7 3	L7 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSSC-5L.R1.fq.gz TSSC-5L.R2.fq.gz	fastq fastq	6846271200.0	22820904.0	TSSC 5L.R1.fq.gz	0:150 1:150	A:1704275603;C:1639794530;G:1792628691;T:1709317043;N:255333	150	150	1704275603	1639794530	1792628691	1709317043	255333	SRX24807384	SRS21522256	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32516	32516	SRR29290256	SRX24807383	SRS21522255	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	Control parallel 3	liver transcriptome	L1 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal	Zebrafish liver	L1 3	L1 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		FCFC1-3L.R1.fq.gz FCFC1-3L.R2.fq.gz	fastq fastq	6360438000.0	21201460.0	FCFC1 3L.R1.fq.gz	0:150 1:150	A:1591177652;C:1544470038;G:1615057708;T:1609485267;N:247335	150	150	1591177652	1544470038	1615057708	1609485267	247335	SRX24807383	SRS21522255	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32517	32517	SRR29290257	SRX24807382	SRS21522254	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 2	liver transcriptome	L7 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L7 2	L7 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSSB-3L.R1.fq.gz TSSB-3L.R2.fq.gz	fastq fastq	6285285600.0	20950952.0	TSSB 3L.R1.fq.gz	0:150 1:150	A:1584093051;C:1516123512;G:1599998121;T:1584824364;N:246552	150	150	1584093051	1516123512	1599998121	1584824364	246552	SRX24807382	SRS21522254	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32518	32518	SRR29290258	SRX24807381	SRS21522253	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 1	liver transcriptome	L7 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 25\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles 40 60 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L7 1	L7 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSSA-1L.R1.fq.gz TSSA-1L.R2.fq.gz	fastq fastq	6078740100.0	20262467.0	TSSA 1L.R1.fq.gz	0:150 1:150	A:1530149533;C:1486474895;G:1528868563;T:1533006599;N:240510	150	150	1530149533	1486474895	1528868563	1533006599	240510	SRX24807381	SRS21522253	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32519	32519	SRR29290259	SRX24807380	SRS21522252	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 3	liver transcriptome	L6 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L6 3	L6 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSFC1-3L.R1.fq.gz TSFC1-3L.R2.fq.gz	fastq fastq	6857466600.0	22858222.0	TSFC1 3L.R1.fq.gz	0:150 1:150	A:1755136176;C:1642995302;G:1688825155;T:1770233592;N:276375	150	150	1755136176	1642995302	1688825155	1770233592	276375	SRX24807380	SRS21522252	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32520	32520	SRR29290260	SRX24807379	SRS21522251	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 2	liver transcriptome	L6 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L6 2	L6 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSFB1-3L.R1.fq.gz TSFB1-3L.R2.fq.gz	fastq fastq	7250329800.0	24167766.0	TSFB1 3L.R1.fq.gz	0:150 1:150	A:1825803037;C:1766132142;G:1813762639;T:1844348502;N:283480	150	150	1825803037	1766132142	1813762639	1844348502	283480	SRX24807379	SRS21522251	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32521	32521	SRR29290261	SRX24807378	SRS21522250	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 1	liver transcriptome	L6 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 10\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 14\|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L6 1	L6 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TSFA1-3L.R1.fq.gz TSFA1-3L.R2.fq.gz	fastq fastq	6257752800.0	20859176.0	TSFA1 3L.R1.fq.gz	0:150 1:150	A:1588621972;C:1490176001;G:1573465475;T:1605244426;N:244926	150	150	1588621972	1490176001	1573465475	1605244426	244926	SRX24807378	SRS21522250	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32522	32522	SRR29290262	SRX24807377	SRS21522249	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 3	liver transcriptome	L5 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 13\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L5 3	L5 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMSC-5L.R1.fq.gz TMSC-5L.R2.fq.gz	fastq fastq	6227549100.0	20758497.0	TMSC 5L.R1.fq.gz	0:150 1:150	A:1601663321;C:1467885504;G:1549957271;T:1607796578;N:246426	150	150	1601663321	1467885504	1549957271	1607796578	246426	SRX24807377	SRS21522249	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32523	32523	SRR29290263	SRX24807376	SRS21522248	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 2	liver transcriptome	L5 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L5 2	L5 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMSB-3L.R1.fq.gz TMSB-3L.R2.fq.gz	fastq fastq	5889087600.0	19630292.0	TMSB 3L.R1.fq.gz	0:150 1:150	A:1507527640;C:1395223794;G:1475557797;T:1510549619;N:228750	150	150	1507527640	1395223794	1475557797	1510549619	228750	SRX24807376	SRS21522248	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32524	32524	SRR29290264	SRX24807375	SRS21522247	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	30 days experimental group parallel 1	liver transcriptome	L5 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 24\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L5 1	L5 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMSA-1L.R1.fq.gz TMSA-1L.R2.fq.gz	fastq fastq	6438780300.0	21462601.0	TMSA 1L.R1.fq.gz	0:150 1:150	A:1651115385;C:1542448300;G:1589631411;T:1655336061;N:249143	150	150	1651115385	1542448300	1589631411	1655336061	249143	SRX24807375	SRS21522247	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32525	32525	SRR29290265	SRX24807374	SRS21522246	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 3	liver transcriptome	L4 3	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 16\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L4 3	L4 3	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMFC1-3L.R1.fq.gz TMFC1-3L.R2.fq.gz	fastq fastq	6083883300.0	20279611.0	TMFC1 3L.R1.fq.gz	0:150 1:150	A:1510698562;C:1511134044;G:1540128451;T:1521679717;N:242526	150	150	1510698562	1511134044	1540128451	1521679717	242526	SRX24807374	SRS21522246	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32526	32526	SRR29290266	SRX24807373	SRS21522245	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	15 days experimental group parallel 2	liver transcriptome	L4 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 09\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 15\|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days\|BioSampleModel:Model organism or animal	Zebrafish liver	L4 2	L4 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		TMFB1-3L.R1.fq.gz TMFB1-3L.R2.fq.gz	fastq fastq	5908013700.0	19693379.0	TMFB1 3L.R1.fq.gz	0:150 1:150	A:1507137134;C:1415511620;G:1463261753;T:1521838130;N:265063	150	150	1507137134	1415511620	1463261753	1521838130	265063	SRX24807373	SRS21522245	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32527	32527	SRR29290267	SRX24807372	SRS21522244	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	Control parallel 2	liver transcriptome	L1 2	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 12\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal	Zebrafish liver	L1 2	L1 2	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		FCFB1-3L.R1.fq.gz FCFB1-3L.R2.fq.gz	fastq fastq	6637856700.0	22126189.0	FCFB1 3L.R1.fq.gz	0:150 1:150	A:1714779556;C:1575842801;G:1628771136;T:1718209685;N:253522	150	150	1714779556	1575842801	1628771136	1718209685	253522	SRX24807372	SRS21522244	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
32528	32528	SRR29290268	SRX24807371	SRS21522243	SRP511901	PRJNA1120203	Study of liver transcriptome in zebrafish May 29 '24	PRJNA1120203	Other	Liver of the transcriptome data from zebrafish exposed to small car tire wear particles	Control parallel 1	liver transcriptome	L1 1	strain:not applicable\|isolate:not applicable\|breed:zebrafish\|cultivar:not applicable\|ecotype:not applicable\|age:3 month\|dev stage:3 month\|collection date:2023 08 11\|geo loc name:China\|sex:not collected\|tissue:liver\|birth date:2023 05 11\|experiment description:Sample from control group\|BioSampleModel:Model organism or animal	Zebrafish liver	L1 1	L1 1	Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform generating paired end reads.		OTHER	METATRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP511901		FCFA1-3L.R1.fq.gz FCFA1-3L.R2.fq.gz	fastq fastq	7360809900.0	24536033.0	FCFA1 3L.R1.fq.gz	0:150 1:150	A:1885247052;C:1777296186;G:1818891778;T:1879185198;N:189686	150	150	1885247052	1777296186	1818891778	1879185198	189686	SRX24807371	SRS21522243	SRA1889615	Qingdao University of Science and technology\|College of marine science and biological engineeri	Qingdao University of Science and technology												B	B	biological fallback assumption	illumina	novaseq_era	unknown	other	unknown	bulk	unknown	unknown	China	2024-06-05	Adult	Adult	Liver	Liver and Biliary System
35452	35452	SRR32815440	SRX28098911	SRS24455832	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				T4Danio rerio	strain:T4\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T4\|BioSampleModel:Model organism or animal	T4	T4	T4	T4		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		T4_1.fq.gz T4_2.fq.gz	fastq fastq	6608651700.0	22028839.0	T4 1.fq.gz	0:150 1:150	A:1815401801;C:1489859310;G:1499379699;T:1804010890;N:0	150	150	1815401801	1489859310	1499379699	1804010890	0	SRX28098911	SRS24455832	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35453	35453	SRR32815441	SRX28098910	SRS24455831	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				T3Danio rerio	strain:T3\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T3\|BioSampleModel:Model organism or animal	T3	T3	T3	T3		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		T3_1.fq.gz T3_2.fq.gz	fastq fastq	6656167200.0	22187224.0	T3 1.fq.gz	0:150 1:150	A:1840552276;C:1489247530;G:1499297584;T:1827069810;N:0	150	150	1840552276	1489247530	1499297584	1827069810	0	SRX28098910	SRS24455831	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35454	35454	SRR32815442	SRX28098909	SRS24455830	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				T2Danio rerio	strain:T2\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T2\|BioSampleModel:Model organism or animal	T2	T2	T2	T2		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		T2_1.fq.gz T2_2.fq.gz	fastq fastq	6622204800.0	22074016.0	T2 1.fq.gz	0:150 1:150	A:1834396150;C:1480094606;G:1490046882;T:1817667162;N:0	150	150	1834396150	1480094606	1490046882	1817667162	0	SRX28098909	SRS24455830	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35455	35455	SRR32815443	SRX28098908	SRS24455829	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				T1Danio rerio	strain:T1\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:T1\|BioSampleModel:Model organism or animal	T1	T1	T1	T1		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		T1_1.fq.gz T1_2.fq.gz	fastq fastq	6626122500.0	22087075.0	T1 1.fq.gz	0:150 1:150	A:1833541012;C:1481665295;G:1491851279;T:1819064914;N:0	150	150	1833541012	1481665295	1491851279	1819064914	0	SRX28098908	SRS24455829	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35456	35456	SRR32815444	SRX28098907	SRS24455828	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				Q4Danio rerio	strain:Q4\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q4\|BioSampleModel:Model organism or animal	Q4	Q4	Q4	Q4		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		Q4_1.fq.gz Q4_2.fq.gz	fastq fastq	6646083600.0	22153612.0	Q4 1.fq.gz	0:150 1:150	A:1823086981;C:1499930776;G:1510718905;T:1812346938;N:0	150	150	1823086981	1499930776	1510718905	1812346938	0	SRX28098907	SRS24455828	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35457	35457	SRR32815445	SRX28098906	SRS24455827	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				Q3Danio rerio	strain:Q3\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q3\|BioSampleModel:Model organism or animal	Q3	Q3	Q3	Q3		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		Q3_1.fq.gz Q3_2.fq.gz	fastq fastq	6683275200.0	22277584.0	Q3 1.fq.gz	0:150 1:150	A:1838068171;C:1503920885;G:1514577234;T:1826708910;N:0	150	150	1838068171	1503920885	1514577234	1826708910	0	SRX28098906	SRS24455827	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35458	35458	SRR32815446	SRX28098905	SRS24455826	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				Q2Danio rerio	strain:Q2\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q2\|BioSampleModel:Model organism or animal	Q2	Q2	Q2	Q2		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		Q2_1.fq.gz Q2_2.fq.gz	fastq fastq	6612253800.0	22040846.0	Q2 1.fq.gz	0:150 1:150	A:1821750297;C:1484945478;G:1495582042;T:1809975983;N:0	150	150	1821750297	1484945478	1495582042	1809975983	0	SRX28098905	SRS24455826	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined
35459	35459	SRR32815447	SRX28098904	SRS24455825	SRP572346	PRJNA1240620	The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes	PRJNA1240620	Other				Q1Danio rerio	strain:Q1\|age:96hpf\|collection date:2023 12 20\|geo loc name:China: Xiangyang\|sex:missing\|tissue:Tissue of juvenile fish\|replicate:Q1\|BioSampleModel:Model organism or animal	Q1	Q1	Q1	Q1		RNA-Seq	METATRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP572346		Q1_1.fq.gz Q1_2.fq.gz	fastq fastq	6725919900.0	22419733.0	Q1 1.fq.gz	0:150 1:150	A:1845653740;C:1518697545;G:1530630124;T:1830938491;N:0	150	150	1845653740	1518697545	1530630124	1830938491	0	SRX28098904	SRS24455825	SRA2098321	Wuhan University of Science and Technology\|School of Medicine	Wuhan University of Science and Technology												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2025-03-22	Larval	Larval	Undetermined	Undetermined

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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");;