rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,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.spot_descriptor,experiment.study_ref,run.title,run.attributes,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.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 52242,SRR9047069,SRX5823596,SRS4751717,SRP198207,PRJNA542583,Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation,PRJNA542583,Other,Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis.,,,,stdMO PBS,stdMO PBS,,strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal,,,,,,,,,tspan RNA seq,uniprot,uniprot,RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,BGISEQ,BGISEQ-500,,SRP198207,,,161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz,fastq,633650654.0,12931646.0,161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz,0:49 1:0,A:165787428;C:152969494;G:145599180;T:169168973;N:125579,49,0,,,165787428,152969494,145599180,169168973,125579,SRX5823596,SRS4751717,SRA885639,Tsinghua University|School of Life Sciences,Tsinghua University,1,0.93004,,0.09559,,0.753,,0.47488,,49,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2019-05-30,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 57168,SRR11237928,SRX7849591,SRS6259054,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 7hpf Dome,GSM4379949,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,MZ 7hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:7 hpf nup85 / ;nup133 / ,GSM4379949,GSM4379949: MZ 7hpf Dome; Danio rerio; RNA Seq,GSM4379949,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379949,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_7h_Dome_1.fq.gz,fastq,1065702100.0,21314042.0,GSM4379949 r1,0:50 1:0,A:283324952;C:247492025;G:242059243;T:291819466;N:1006414,50,0,,,283324952,247492025,242059243,291819466,1006414,SRX7849591,SRS6259054,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.9445,,0.07752,,0.72565,,0.4828,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Gastrula,Embryo,Embryo Imprecise,All anatomical structures 57169,SRR11237927,SRX7849590,SRS6259053,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,MZ 4.3hpf 1k,GSM4379948,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,MZ 4.3hpf 1k,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf nup85 / ;nup133 / ,GSM4379948,GSM4379948: MZ 4.3hpf 1k; Danio rerio; RNA Seq,GSM4379948,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379948,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,MZ_4.3h_1k_1.fq.gz,fastq,1059959500.0,21199190.0,GSM4379948 r1,0:50 1:0,A:278456455;C:249622199;G:244991579;T:285847713;N:1041554,50,0,,,278456455,249622199,244991579,285847713,1041554,SRX7849590,SRS6259053,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94882,,0.03659,,0.74361,,0.48435,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 57170,SRR11237926,SRX7849589,SRS6259052,SRP251591,PRJNA610302,Transcriptome analysis of wild type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development,GSE146394,Transcriptome Analysis,To study the function of zebrafish nuclear pores during early embryogenesis we generated maternal zygotic double mutant of nup85;nup133 MZnup85;nup133 using CRISPR/Cas9 and report the transcriptome wide changes in comparison to wild type WT embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal to zygotic transition. Overall design: mRNA profile of zebrafish WT and MZnup85;nup133 embryos at 4.3 hpf or at stage with dome morphology,,,,WT 4.3hpf Dome,GSM4379947,,source name:whole mount embryo|strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,WT 4.3hpf Dome,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,strain:AB|tissue:whole mount embryo|developmental stage:4.3 hpf type,GSM4379947,GSM4379947: WT 4.3hpf Dome; Danio rerio; RNA Seq,GSM4379947,,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,GEO Accession:GSM4379947,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP251591,,,WT_4.3h_Dome_1.fq.gz,fastq,1058158950.0,21163179.0,GSM4379947 r1,0:50 1:0,A:279307143;C:247873321;G:244308380;T:285580565;N:1089541,50,0,,,279307143,247873321,244308380,285580565,1089541,SRX7849589,SRS6259052,SRA1051151,GEO,"School of life science, Tsinghua University",1,0.94374,,0.05294,,0.74164,,0.48705,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2020-03-04,Blastula,Embryo,Embryo Imprecise,All anatomical structures 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,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,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,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,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,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,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,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,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,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,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 61503,SRR12780056,SRX9249644,SRS7482118,SRP286526,PRJNA667677,Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish,GSE159087,Transcriptome Analysis,Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.,,,,phf tMO 4.7h,GSM4819005,,tissue:embryos|strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,phf tMO 4.7h,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples,embryos,Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Embryos were cultured in the holfretor water.,strain:Tuebingen|genotype/variation:phf14 MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,GSM4819005,GSM4819005: phf tMO 4.7h; Danio rerio; RNA Seq,GSM4819005,,1,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4819005,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP286526,,,phf_tMO_4.7h.fq.gz,fastq,1169147800.0,23382956.0,GSM4819005 r1,0:50,A:311605612;C:272452820;G:269040332;T:316049036;N:0,50,,,,311605612,272452820,269040332,316049036,0,SRX9249644,SRS7482118,SRA1139165,GEO,"Haitao Li, School of medicine, Tsinghua University",1,0.94966,,0.07252,,0.73651,,0.49931,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2020-10-06,Blastula,Embryo,Embryo Imprecise,All anatomical structures 61504,SRR12780055,SRX9249643,SRS7482117,SRP286526,PRJNA667677,Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish,GSE159087,Transcriptome Analysis,Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf.,,,,std MO 4.7h,GSM4819004,,tissue:embryos|strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,std MO 4.7h,Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples,embryos,Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,Embryos were cultured in the holfretor water.,strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos,GSM4819004,GSM4819004: std MO 4.7h; Danio rerio; RNA Seq,GSM4819004,,1,Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM4819004,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP286526,,,std_MO_4.7h.fq.gz,fastq,1169210150.0,23384203.0,GSM4819004 r1,0:50,A:311848924;C:271805947;G:268541126;T:317014153;N:0,50,,,,311848924,271805947,268541126,317014153,0,SRX9249643,SRS7482117,SRA1139165,GEO,"Haitao Li, School of medicine, Tsinghua University",1,0.94838,,0.07833,,0.74192,,0.48213,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2020-10-06,Blastula,Embryo,Embryo Imprecise,All anatomical structures 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,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,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,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,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,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 71312,SRR21487520,SRX17491012,SRS15043328,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos WGA treated 5 hpf dome like stage,GSM6562796,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,zebrafish early embryos WGA treated 5 hpf dome like stage,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,GSM6562796,GSM6562796: zebrafish early embryos WGA treated 5 hpf dome like stage; Danio rerio; RNA Seq,GSM6562796 r1,GSM6562796,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WGA_5h.fq.gz,fastq,1059386400.0,21187728.0,GSM6562796 r1,0:50 1:0,A:277040646;C:250203561;G:245816009;T:285209577;N:1116607,50,0,,,277040646,250203561,245816009,285209577,1116607,SRX17491012,SRS15043328,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94419,,0.03669,,0.74919,,0.48293,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71313,SRR21487521,SRX17491011,SRS15043327,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos WGA treated 4.3 hpf,GSM6562795,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,zebrafish early embryos WGA treated 4.3 hpf,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:0.65 ng WGA injected at 1 cell stage,GSM6562795,GSM6562795: zebrafish early embryos WGA treated 4.3 hpf; Danio rerio; RNA Seq,GSM6562795 r1,GSM6562795,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WGA_4.3h.fq.gz,fastq,1062790650.0,21255813.0,GSM6562795 r1,0:50 1:0,A:277911032;C:251212426;G:246864055;T:285783146;N:1019991,50,0,,,277911032,251212426,246864055,285783146,1019991,SRX17491011,SRS15043327,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94436,,0.0365,,0.7488,,0.47923,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures 71314,SRR21487522,SRX17491010,SRS15043326,SRP396256,PRJNA878480,Effect of nuclear pore complex NPC blockage by WGA treatment on zygotic genome activation ZGA during zebrafish early development,GSE212929,Transcriptome Analysis,To investigate the function of nuclear pore complex NPC in the regulation of zygotic genome activation ZGA we microinjected medium dosage of WGA in zebrafish embryos at xxx cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA seq of control or WGA treated embryo at comparable developmental time point 4.3 hpf or develomental stage dome. Overall design: Comparative gene expression profiling analysis of RNA seq data for zebrafish control embryo at 4.3 hpf of dome stage and WGA treated embryos at 4.3 hpf developmental time matched or 5 hpf dome like stage.,,pubmed:36493774,,zebrafish early embryos wildtype 4.3 hpf dome stage,GSM6562794,,source name:whole mount embryo|tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A,zebrafish early embryos wildtype 4.3 hpf dome stage,BGISEQ 500 platform was used for base calling Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence on trimmomatic software v0.36 with paramwters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50 then mapped to GRCz11 whole genome using Bowtie2 v2.2.5 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 Fragments Per Kilobase of exon per Megabase of library size FPKM were calculated using software RSEM v1.2.8 from Langmead B. et al. Nat. Methods 2012 and Li B. & Dewey C. N. BMC Bioinformatics 2011. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,whole mount embryo,1 nl WGA of 0.65 ng/nl dissolved in nuclease free water was microinjected into yolk of embryos at xxx cell stage.,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,tissue:whole mount embryo|cell line:early embryo|cell type:embryonic cell|genotype:wildtype|treatment:N/A,GSM6562794,GSM6562794: zebrafish early embryos wildtype 4.3 hpf dome stage; Danio rerio; RNA Seq,GSM6562794 r1,GSM6562794,1,total RNAs were extracted from dechorionated whole embryos with RNeasy Mini Kit Qiagen RNA libraries were prepared for sequencing using standard protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP396256,,,WT_4.3h.fq.gz,fastq,1063999350.0,21279987.0,GSM6562794 r1,0:50 1:0,A:280657534;C:249334239;G:244705183;T:288194607;N:1107787,50,0,,,280657534,249334239,244705183,288194607,1107787,SRX17491010,SRS15043326,SRA1496611,"School of life science, Tsinghua University","School of life science, Tsinghua University",1,0.94283,,0.06247,,0.73474,,0.49113,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2022-09-08,Blastula,Embryo,Embryo Imprecise,All anatomical structures