metadata: run_metadata: 35 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue

35 rows where experiment.library_layout = "PAIRED", experiment.platform = "BGISEQ" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
55655	55655	SRR10674410	SRX7351703	SRS5811186	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 100 1	isolate:biologocal replicate 10\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050110	bps050110	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_1_1.fq.gz BPS_100_1_2.fq.gz	fastq fastq	6958801200.0	69588012.0	BPS 100 1 1.fq.gz	0:100 1:100	A:1852139865;C:1635606671;G:1596180575;T:1874072794;N:801295	100	100	1852139865	1635606671	1596180575	1874072794	801295	SRX7351703	SRS5811186	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94716	0.09824	0.68475	0.47195	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55656	55656	SRR10674411	SRX7351702	SRS5811185	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 10 3	isolate:biologocal replicate 9\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050109	bps050109	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_3_1.fq.gz BPS_10_3_2.fq.gz	fastq fastq	6969574800.0	69695748.0	BPS 10 3 1.fq.gz	0:100 1:100	A:1860393053;C:1631995190;G:1597357772;T:1879188120;N:640665	100	100	1860393053	1631995190	1597357772	1879188120	640665	SRX7351702	SRS5811185	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94597	0.10542	0.68016	0.4666	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55657	55657	SRR10674412	SRX7351701	SRS5811182	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 10 2	isolate:biologocal replicate 8\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050108	bps050108	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_2_1.fq.gz BPS_10_2_2.fq.gz	fastq fastq	6709340400.0	67093404.0	BPS 10 2 1.fq.gz	0:100 1:100	A:2036224090;C:1319652145;G:1297564214;T:2055258677;N:641274	100	100	2036224090	1319652145	1297564214	2055258677	641274	SRX7351701	SRS5811182	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.87778	0.38111	0.71543	0.56061	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55658	55658	SRR10674413	SRX7351700	SRS5811181	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 10 1	isolate:biologocal replicate 7\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050107	bps050107	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_10_1_1.fq.gz BPS_10_1_2.fq.gz	fastq fastq	6717746800.0	67177468.0	BPS 10 1 1.fq.gz	0:100 1:100	A:1787637885;C:1578942212;G:1548400030;T:1802147201;N:619472	100	100	1787637885	1578942212	1548400030	1802147201	619472	SRX7351700	SRS5811181	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94726	0.10123	0.68919	0.45234	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55659	55659	SRR10674414	SRX7351699	SRS5811184	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1 3	isolate:biologocal replicate 6\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050106	bps050106	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_3_2.fq.gz BPS_1_3_1.fq.gz	fastq fastq	6726522800.0	67265228.0	BPS 1 3 1.fq.gz	0:100 1:100	A:1789486049;C:1582069064;G:1548432478;T:1805913744;N:621465	100	100	1789486049	1582069064	1548432478	1805913744	621465	SRX7351699	SRS5811184	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.9465	0.09858	0.68442	0.45032	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55660	55660	SRR10674415	SRX7351698	SRS5811180	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1 2	isolate:biologocal replicate 5\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050105	bps050105	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_2_2.fq.gz BPS_1_2_1.fq.gz	fastq fastq	6959685000.0	69596850.0	BPS 1 2 1.fq.gz	0:100 1:100	A:1914426129;C:1574998719;G:1542052351;T:1927550147;N:657654	100	100	1914426129	1574998719	1542052351	1927550147	657654	SRX7351698	SRS5811180	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94034	0.14574	0.69934	0.47033	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55661	55661	SRR10674416	SRX7351697	SRS5811183	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1 1	isolate:biologocal replicate 4\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050104	bps050104	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1_1_1.fq.gz BPS_1_1_2.fq.gz	fastq fastq	7040826400.0	70408264.0	BPS 1 1 1.fq.gz	0:100 1:100	A:1915125100;C:1612334047;G:1578924466;T:1933922418;N:520369	100	100	1915125100	1612334047	1578924466	1933922418	520369	SRX7351697	SRS5811183	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94114	0.13158	0.68903	0.47739	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55662	55662	SRR10674417	SRX7351696	SRS5811179	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 0 1 3	isolate:biologocal replicate 3\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050103	bps050103	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_3_1.fq.gz BPS_0_1_3_2.fq.gz	fastq fastq	6992676800.0	69926768.0	BPS 0 1 3 1.fq.gz	0:100 1:100	A:1860627581;C:1643489002;G:1610508221;T:1877536968;N:515028	100	100	1860627581	1643489002	1610508221	1877536968	515028	SRX7351696	SRS5811179	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94485	0.101	0.68314	0.45711	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55663	55663	SRR10674418	SRX7351695	SRS5811178	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				Cntrol3	isolate:biologocal replicate 18\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050118	bps050118	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol3_1.fq.gz Cntrol3_2.fq.gz	fastq fastq	6742983200.0	67429832.0	Cntrol3 1.fq.gz	0:100 1:100	A:1801392073;C:1577630219;G:1545614005;T:1817857809;N:489094	100	100	1801392073	1577630219	1545614005	1817857809	489094	SRX7351695	SRS5811178	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94386	0.10779	0.68832	0.45545	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55664	55664	SRR10674419	SRX7351694	SRS5811177	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				Cntrol2	isolate:biologocal replicate 17\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050117	bps050117	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol2_1.fq.gz Cntrol2_2.fq.gz	fastq fastq	6750661000.0	67506610.0	Cntrol2 1.fq.gz	0:100 1:100	A:1796606666;C:1585909518;G:1556014239;T:1811284557;N:846020	100	100	1796606666	1585909518	1556014239	1811284557	846020	SRX7351694	SRS5811177	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94397	0.10007	0.68708	0.47779	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55665	55665	SRR10674420	SRX7351693	SRS5811174	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				Cntrol1	isolate:biologocal replicate 16\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050116	bps050116	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	Cntrol1_1.fq.gz Cntrol1_2.fq.gz	fastq fastq	6766663000.0	67666630.0	Cntrol1 1.fq.gz	0:100 1:100	A:1825736389;C:1564390057;G:1532835305;T:1842876742;N:824507	100	100	1825736389	1564390057	1532835305	1842876742	824507	SRX7351693	SRS5811174	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94047	0.12338	0.68893	0.46407	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55666	55666	SRR10674421	SRX7351692	SRS5811176	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1000 3	isolate:biologocal replicate 15\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050115	bps050115	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_3_1.fq.gz BPS_1000_3_2.fq.gz	fastq fastq	6507622200.0	65076222.0	BPS 1000 3 1.fq.gz	0:100 1:100	A:1735402948;C:1525938362;G:1493787016;T:1751945676;N:548198	100	100	1735402948	1525938362	1493787016	1751945676	548198	SRX7351692	SRS5811176	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94304	0.10593	0.6842	0.46348	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55667	55667	SRR10674422	SRX7351691	SRS5811173	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1000 2	isolate:biologocal replicate 14\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050114	bps050114	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_2_1.fq.gz BPS_1000_2_2.fq.gz	fastq fastq	6740712000.0	67407120.0	BPS 1000 2 1.fq.gz	0:100 1:100	A:1816870993;C:1562402111;G:1527381283;T:1833284067;N:773546	100	100	1816870993	1562402111	1527381283	1833284067	773546	SRX7351691	SRS5811173	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94327	0.11511	0.70033	0.4551	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55668	55668	SRR10674423	SRX7351690	SRS5811175	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 1000 1	isolate:biologocal replicate 13\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050113	bps050113	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_1000_1_1.fq.gz BPS_1000_1_2.fq.gz	fastq fastq	6727750400.0	67277504.0	BPS 1000 1 1.fq.gz	0:100 1:100	A:1803578734;C:1568712705;G:1535618959;T:1819016739;N:823263	100	100	1803578734	1568712705	1535618959	1819016739	823263	SRX7351690	SRS5811175	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94457	0.1118	0.69087	0.46815	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55669	55669	SRR10674424	SRX7351689	SRS5811172	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 100 3	isolate:biologocal replicate 12\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050112	bps050112	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_3_1.fq.gz BPS_100_3_2.fq.gz	fastq fastq	6962431800.0	69624318.0	BPS 100 3 1.fq.gz	0:100 1:100	A:1865300693;C:1624120289;G:1585691091;T:1886538935;N:780792	100	100	1865300693	1624120289	1585691091	1886538935	780792	SRX7351689	SRS5811172	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94581	0.10195	0.68288	0.47174	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55670	55670	SRR10674425	SRX7351688	SRS5811171	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 100 2	isolate:biologocal replicate 11\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050111	bps050111	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_100_2_1.fq.gz BPS_100_2_2.fq.gz	fastq fastq	7201035800.0	72010358.0	BPS 100 2 1.fq.gz	0:100 1:100	A:2115590854;C:1489181336;G:1459936470;T:2135514629;N:812511	100	100	2115590854	1489181336	1459936470	2135514629	812511	SRX7351688	SRS5811171	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.90678	0.29289	0.70735	0.49554	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55671	55671	SRR10674426	SRX7351687	SRS5811170	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 0 1 2	isolate:biologocal replicate 2\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050102	bps050102	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_2_1.fq.gz BPS_0_1_2_2.fq.gz	fastq fastq	7022382800.0	70223828.0	BPS 0 1 2 1.fq.gz	0:100 1:100	A:1853514579;C:1663935080;G:1635277415;T:1869136960;N:518766	100	100	1853514579	1663935080	1635277415	1869136960	518766	SRX7351687	SRS5811170	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94712	0.09313	0.6814	0.47256	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
55672	55672	SRR10674427	SRX7351686	SRS5811167	SRP237283	PRJNA595113	Transcriptomic responses of Bisphenol S on zebrafish	PRJNA595113	Other	To better understand the multiple interacting molecular mechanisms that are altered during BPS exposure global transcriptome sequencing RNA Seq was performed in embryonic fish to quantify expression levels of transcripts with a high sensitivity and broad genome coverage post BPS treatment19. To better understand sensitivities of fish to BPS toxicity and the mechanisms that regulate expression of transcripts altered by BPS exposure we evaluated morphological and transcriptional effects in using environmentally relevant concentrations.				BPS 0 1 1	isolate:biologocal replicate 1\|age:120hpf\|sex:not collected\|tissue:embryo\|collection date:2018 05 01\|geo loc name:China:Guangdong\|BioSampleModel:Model organism or animal									Transcriptomic responses of Bisphenol S	bps050101	bps050101	An Agilent 2100 bioanalyzer chip was used to determine RNA integrity score Agilent Santa Clara CA USA with only high quality RNA samples 28 S:18 S=2.02.2 RIN>9.0 used to construct libraries following a standardized procedure at the Beijing Genome Institute BGI; Shenzhen China . The libraries were sequenced at the Beijing Genomics Institute BGI Shenzhen China on a BGISEQ500 platform with 50 bp single end reads under three replicates per treatment group.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	BGISEQ	BGISEQ-500	SRP237283	BPS_0_1_1_1.fq.gz BPS_0_1_1_2.fq.gz	fastq fastq	7013900400.0	70139004.0	BPS 0 1 1 1.fq.gz	0:100 1:100	A:1885826391;C:1629114228;G:1597181244;T:1901261511;N:517026	100	100	1885826391	1629114228	1597181244	1901261511	517026	SRX7351686	SRS5811167	SRA1010884	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.94226	0.11616	0.69014	0.45679	100	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2019-12-12	Larval	Larval	Embryo Imprecise	All anatomical structures
59480	59480	SRR11922874	SRX8468588	SRS6769276	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep6	GSM4590772	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep6	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590772	GSM4590772: zebrafish embryo Aldh3a1 KO rep6; Danio rerio; RNA Seq	GSM4590772		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590772	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	12_aldh3a1----homo-48hpf-6_1.fq.gz 12_aldh3a1----homo-48hpf-6_2.fq.gz	fastq fastq	4660603600.0	46606036.0	GSM4590772 r1	0:100 1:100	A:1396899993;C:924291840;G:902974172;T:1436437595;N:0	100	100	1396899993	924291840	902974172	1436437595	0	SRX8468588	SRS6769276	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90281	0.2525	0.75943	0.62165	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59481	59481	SRR11922873	SRX8468587	SRS6769275	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep5	GSM4590771	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590771	GSM4590771: zebrafish embryo Aldh3a1 KO rep5; Danio rerio; RNA Seq	GSM4590771		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590771	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	11_aldh3a1----homo-48hpf-5_1.fq.gz 11_aldh3a1----homo-48hpf-5_2.fq.gz	fastq fastq	3919649800.0	39196498.0	GSM4590771 r1	0:100 1:100	A:1203194756;C:742776682;G:744133378;T:1229544984;N:0	100	100	1203194756	742776682	744133378	1229544984	0	SRX8468587	SRS6769275	SRA1083013	GEO	ZMF, University Heidelberg	1	0.86745	0.31349	0.76702	0.63864	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59482	59482	SRR11922872	SRX8468586	SRS6769274	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep4	GSM4590770	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590770	GSM4590770: zebrafish embryo Aldh3a1 KO rep4; Danio rerio; RNA Seq	GSM4590770		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590770	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	10_aldh3a1----homo-48hpf-4_2.fq.gz 10_aldh3a1----homo-48hpf-4_1.fq.gz	fastq fastq	4549625000.0	45496250.0	GSM4590770 r1	0:100 1:100	A:1345145181;C:925949636;G:905779914;T:1372750269;N:0	100	100	1345145181	925949636	905779914	1372750269	0	SRX8468586	SRS6769274	SRA1083013	GEO	ZMF, University Heidelberg	1	0.9117	0.23055	0.72545	0.50968	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59483	59483	SRR11922871	SRX8468585	SRS6769273	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep3	GSM4590769	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590769	GSM4590769: zebrafish embryo Aldh3a1 KO rep3; Danio rerio; RNA Seq	GSM4590769		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590769	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	9_aldh3a1----homo-48hpf-3_1.fq.gz 9_aldh3a1----homo-48hpf-3_2.fq.gz	fastq fastq	4194991600.0	41949916.0	GSM4590769 r1	0:100 1:100	A:1258296885;C:833884600;G:816600639;T:1286209476;N:0	100	100	1258296885	833884600	816600639	1286209476	0	SRX8468585	SRS6769273	SRA1083013	GEO	ZMF, University Heidelberg	1	0.89574	0.28139	0.73397	0.56688	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59484	59484	SRR11922870	SRX8468584	SRS6769272	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep2	GSM4590768	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590768	GSM4590768: zebrafish embryo Aldh3a1 KO rep2; Danio rerio; RNA Seq	GSM4590768		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590768	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	8_aldh3a1----homo-48hpf-2_1.fq.gz 8_aldh3a1----homo-48hpf-2_2.fq.gz	fastq fastq	5097901600.0	50979016.0	GSM4590768 r1	0:100 1:100	A:1487281075;C:1055394796;G:1035616985;T:1519608744;N:0	100	100	1487281075	1055394796	1035616985	1519608744	0	SRX8468584	SRS6769272	SRA1083013	GEO	ZMF, University Heidelberg	1	0.92556	0.18622	0.73026	0.5187	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59485	59485	SRR11922869	SRX8468583	SRS6769271	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo Aldh3a1 KO rep1	GSM4590767	source name:zebrafish embryo\|genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	zebrafish embryo Aldh3a1 KO rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:aldh3a1 KO\|tissue:embryo\|age:48 hpf	GSM4590767	GSM4590767: zebrafish embryo Aldh3a1 KO rep1; Danio rerio; RNA Seq	GSM4590767		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590767	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	7_aldh3a1----homo-48hpf-1_1.fq.gz 7_aldh3a1----homo-48hpf-1_2.fq.gz	fastq fastq	5075421000.0	50754210.0	GSM4590767 r1	0:100 1:100	A:1523744143;C:1008915874;G:985443760;T:1557317223;N:0	100	100	1523744143	1008915874	985443760	1557317223	0	SRX8468583	SRS6769271	SRA1083013	GEO	ZMF, University Heidelberg	1	0.90167	0.27915	0.75879	0.6673	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59486	59486	SRR11922868	SRX8468582	SRS6769270	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep5	GSM4590766	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep5	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590766	GSM4590766: zebrafish embryo wildtype rep5; Danio rerio; RNA Seq	GSM4590766		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590766	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	6_aldh3a1+-+-wt-48hpf-R_1.fq.gz 6_aldh3a1+-+-wt-48hpf-R_2.fq.gz	fastq fastq	5097636600.0	50976366.0	GSM4590766 r1	0:100 1:100	A:1402424015;C:1146863463;G:1121174200;T:1427174922;N:0	100	100	1402424015	1146863463	1121174200	1427174922	0	SRX8468582	SRS6769270	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95115	0.09816	0.69781	0.46194	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59487	59487	SRR11922867	SRX8468581	SRS6769269	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep4	GSM4590765	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep4	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590765	GSM4590765: zebrafish embryo wildtype rep4; Danio rerio; RNA Seq	GSM4590765		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590765	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	4_aldh3a1+-+-wt-48hpf-4_1.fq.gz 4_aldh3a1+-+-wt-48hpf-4_2.fq.gz	fastq fastq	4847250800.0	48472508.0	GSM4590765 r1	0:100 1:100	A:1351516729;C:1070410976;G:1050113082;T:1375210013;N:0	100	100	1351516729	1070410976	1050113082	1375210013	0	SRX8468581	SRS6769269	SRA1083013	GEO	ZMF, University Heidelberg	1	0.94418	0.12404	0.69374	0.49948	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59488	59488	SRR11922866	SRX8468580	SRS6769268	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep3	GSM4590764	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep3	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590764	GSM4590764: zebrafish embryo wildtype rep3; Danio rerio; RNA Seq	GSM4590764		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590764	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	3_aldh3a1+-+-wt-48hpf-3_1.fq.gz 3_aldh3a1+-+-wt-48hpf-3_2.fq.gz	fastq fastq	5083417400.0	50834174.0	GSM4590764 r1	0:100 1:100	A:1375006484;C:1168556107;G:1139277849;T:1400576960;N:0	100	100	1375006484	1168556107	1139277849	1400576960	0	SRX8468580	SRS6769268	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95419	0.09201	0.69209	0.48244	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59489	59489	SRR11922865	SRX8468579	SRS6769267	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep2	GSM4590763	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep2	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590763	GSM4590763: zebrafish embryo wildtype rep2; Danio rerio; RNA Seq	GSM4590763		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590763	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	2_aldh3a1+-+-wt-48hpf-2_1.fq.gz 2_aldh3a1+-+-wt-48hpf-2_2.fq.gz	fastq fastq	5089646400.0	50896464.0	GSM4590763 r1	0:100 1:100	A:1384714450;C:1161015785;G:1138313445;T:1405602720;N:0	100	100	1384714450	1161015785	1138313445	1405602720	0	SRX8468579	SRS6769267	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95309	0.09301	0.69798	0.48524	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
59490	59490	SRR11922864	SRX8468578	SRS6769266	SRP265910	PRJNA637219	Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype and aldh3a1 / Zebrafish Embryo Transcriptomes	GSE151770	Transcriptome Analysis	Our previous experiments showed the function of Aldh3a1 was related to pancreas and insulin secretion and knockout of Aldh3a1 led to destoryed pancreas. To understand how the impaired pancreas reflects at the transcriptome level we performed full genome RNA Seq between aldh3a1+/+ and aldh3a1 / larvae at 48 hpf.An overview of RNA Seq including quality control principal component analysis PCA volcano plots of regulated genes and Top 20 KEGG pathway analysis showed comparable properties between aldh3a1 mutants and wild type. We found the insulin signalling pathway was reduced significantly via gene set enrichment analysis normalized enrichment score 1.72; p=0.0006. Interestingly endocrine pancreas but not exocrine pancreas development pathway was significantly down regulated in aldh3a1 mutants . Taken together these results further suggest Aldh3a1 as an important regulator in the development morphology and insulin secretion function of primary pancreas. Furthermore we offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. Overall design: mRNA expression profiles of wildtype and aldh3a1 / zebrafish embryo at 48 hpf		pubmed:32980661	zebrafish embryo wildtype rep1	GSM4590762	source name:zebrafish embryo\|genotype:WT\|tissue:embryo\|age:48 hpf	zebrafish embryo wildtype rep1	trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: danRer11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.	zebrafish embryo	Not applicable	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer’s protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	Zebrafish were raised and staged under standard husbandry environment. Embryos were kept in E3 media at 28.5 °C with/without xxx 2.5 ml in 25 ml to suppress pigmentation	genotype:WT\|tissue:embryo\|age:48 hpf	GSM4590762	GSM4590762: zebrafish embryo wildtype rep1; Danio rerio; RNA Seq	GSM4590762		1	Total RNA was isolated from TGfli1:EGFP zebrafish larvae using the RNeasy Mini Kit following the manufacturer's protocol Qiagen. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols	GEO Accession:GSM4590762	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500	SRP265910	1_aldh3a1+-+-wt-48hpf-1_1.fq.gz 1_aldh3a1+-+-wt-48hpf-1_2.fq.gz	fastq fastq	5098267400.0	50982674.0	GSM4590762 r1	0:100 1:100	A:1406329756;C:1147290302;G:1118206731;T:1426440611;N:0	100	100	1406329756	1147290302	1118206731	1426440611	0	SRX8468578	SRS6769266	SRA1083013	GEO	ZMF, University Heidelberg	1	0.95039	0.10482	0.69641	0.47979	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Germany	2020-06-04	Hatching	Embryo	Embryo Imprecise	All anatomical structures
65852	65852	SRR15657174	SRX11954177	SRS9963999	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.156uM 96hpf	GSM5543529	tissue:embryo Cu 0.156uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543529	GSM5543529: embryo Cu 0.156uM 96hpf; Danio rerio; RNA Seq	GSM5543529		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543529	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_96hpf_R1.fastq.gz Cu_0.156uM_96hpf_R2.fastq.gz	fastq fastq	7167443000.0	71674430.0	GSM5543529 r1	0:100 1:100	A:1930084120;C:1646651059;G:1623549050;T:1966203424;N:955347	100	100	1930084120	1646651059	1623549050	1966203424	955347	SRX11954177	SRS9963999	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94339	0.113	0.6549	0.4857	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65853	65853	SRR15657173	SRX11954176	SRS9963998	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.156uM 24hpf	GSM5543528	tissue:embryo Cu 0.156uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.156uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.156uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.156μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543528	GSM5543528: embryo Cu 0.156uM 24hpf; Danio rerio; RNA Seq	GSM5543528		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543528	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.156uM_24hpf_R1.fastq.gz Cu_0.156uM_24hpf_R2.fastq.gz	fastq fastq	7164832400.0	71648324.0	GSM5543528 r1	0:100 1:100	A:1929135591;C:1646939515;G:1617401036;T:1970900148;N:456110	100	100	1929135591	1646939515	1617401036	1970900148	456110	SRX11954176	SRS9963998	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94344	0.10713	0.68919	0.47118	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65854	65854	SRR15657172	SRX11954175	SRS9963997	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.078uM 96hpf	GSM5543527	tissue:embryo Cu 0.078uM 96hpf\|cell type:embryos at 96hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543527	GSM5543527: embryo Cu 0.078uM 96hpf; Danio rerio; RNA Seq	GSM5543527		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543527	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_96hpf_R1.fastq.gz Cu_0.078uM_96hpf_R2.fastq.gz	fastq fastq	7135774800.0	71357748.0	GSM5543527 r1	0:100 1:100	A:1928230196;C:1633490990;G:1605871113;T:1967776814;N:405687	100	100	1928230196	1633490990	1605871113	1967776814	405687	SRX11954175	SRS9963997	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94191	0.11803	0.65614	0.48225	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65855	65855	SRR15657171	SRX11954174	SRS9963995	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Cu 0.078uM 24hpf	GSM5543526	tissue:embryo Cu 0.078uM 24hpf\|cell type:embryos at 24hpf whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Cu 0.078uM 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Cu 0.078uM 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to 0.078μM Cu F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543526	GSM5543526: embryo Cu 0.078uM 24hpf; Danio rerio; RNA Seq	GSM5543526		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543526	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Cu_0.078uM_24hpf_R1.fastq.gz Cu_0.078uM_24hpf_R2.fastq.gz	fastq fastq	6934019600.0	69340196.0	GSM5543526 r1	0:100 1:100	A:1865548284;C:1597354050;G:1569395022;T:1901304271;N:417973	100	100	1865548284	1597354050	1569395022	1901304271	417973	SRX11954174	SRS9963995	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.94389	0.10356	0.68726	0.47794	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65856	65856	SRR15657170	SRX11954173	SRS9963996	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Control 96hpf	GSM5543525	tissue:embryo Control 96hpf\|cell type:embryos at 96hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 96hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 96hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 96hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543525	GSM5543525: embryo Control 96hpf; Danio rerio; RNA Seq	GSM5543525		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543525	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_96hpf_R1.fastq.gz Control_96hpf_R2.fastq.gz	fastq fastq	6698614400.0	66986144.0	GSM5543525 r1	0:100 1:100	A:1816763075;C:1526218454;G:1496202651;T:1858550518;N:879702	100	100	1816763075	1526218454	1496202651	1858550518	879702	SRX11954173	SRS9963996	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93836	0.12432	0.65504	0.47564	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures
65857	65857	SRR15657169	SRX11954172	SRS9963994	SRP334492	PRJNA758398	Parental copper stress induces offspring developmental defects by altering DNA methylation in zebrafish [RNA Seq]	GSE182945	Transcriptome Analysis	Here we describe environmental Cu2+ in promoting zebrafish Danio rerio developmental abnormalities in subsequent generation. This study for the first time demonstrated that: 1. Cu2+ induced alterations in sperm methylome could be passed down to offspring and cause developmental defects in the nervous and digestive system even the Cu2+ concentration is at 10 µg/L the National Quality Standards of fishery water GB11607 89; 2. DNA methylomes of F0 sperms and F1 offspring were altered in a loci specific manner and were correlated with transcriptional expression of genes which function importantly in the development of CNS retina and digestive system development during F1 embryogenesis; 3. Loci specific hypoDMRs in the pmpcb promoter and loci specific hyperDMRs in the crebl2 and tab2 promoters might show adaptive and harmful responses to Cu2+ stresses in next generational inheritance respectively. Those data revealed that Cu2+ induced alterations in sperm methylome may be passed down to offspring and cause the embryonic developmental defects and the resulted inferior seeding suggesting that environmental Cu2+ might pose a dramatic and long lasting threat to the sustainability of fish population and even to humans with imbalanced copper homeostasis. Overall design: Adult zebrafish F0 fish at 3 month of age were divided into three groups: exposure separately to normal water environment control 0.078 µM 5 µg/L and 0.156 µM 10 µg/L Cu for over 21 days with three biological repetitions for each group. Their spawning eggs were collected separately and cultured in normal water environment no Cu added. Briefly 50 60 embryos F1 offspring were collected biasedly based on their phenotypes from each of the 3 groups control; 0.078 µM group; 0.156 µM group at 24 hpf and 96 hpf respectively and lysed by Trizol reagent Ambion Life Technologies for RNA extraction and RNA sequencing RNA Seq.	parent bioproject:PRJNA758396		embryo Control 24hpf	GSM5543524	tissue:embryo Control 24hpf\|cell type:embryos at 24hpf whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	embryo Control 24hpf	Raw reads were filtered for adapter and low quality reads by Trimmomatic Clean reads mapped to the reference genome with TopHat2 The FPKM was calculated by Cufflinks v2.1.1 Genome build: Download the genome from http://ftp.ensembl.org/pub/release 85/fasta/danio rerio/dna/ Supplementary files format and content: tab delimited text files include the FPKM value with echo gene for echo sample	embryo Control 24hpf	50 60 embryos F1 from each group	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	embryos F1 cultured in normal water environment	cell type:embryos at 24hpf hours post fertilization\|treatment:embryos whose parents were exposed to normal water environment F0 fish\|genotype:wild type zebrafish AB at 3 month F0 fish	GSM5543524	GSM5543524: embryo Control 24hpf; Danio rerio; RNA Seq	GSM5543524		1	RNA extraction using Trizol reagent Performed in the Beijing Genomics Institute	GEO Accession:GSM5543524	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	MGISEQ-2000RS	SRP334492	Control_24hpf_R1.fastq.gz Control_24hpf_R2.fastq.gz	fastq fastq	6911559200.0	69115592.0	GSM5543524 r1	0:100 1:100	A:1858569189;C:1592355971;G:1564572369;T:1895593185;N:468486	100	100	1858569189	1592355971	1564572369	1895593185	468486	SRX11954172	SRS9963994	SRA1284991	GEO	college of informatics, Huazhong Agricultural University	1	0.93745	0.09795	0.69059	0.48209	100	B	usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	China	2021-08-27	Multi-stage	Multi-stage	Embryo Imprecise	All anatomical structures

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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");;