metadata: run_metadata: 38 rows where experiment.library_source = "METATRANSCRIPTOMIC", technology = "unknown" and tissue_curation

38 rows where experiment.library_source = "METATRANSCRIPTOMIC", technology = "unknown" and tissue_curation_coarse = "Undetermined"

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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	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
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
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");;