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 48054,SRR7008006,SRX3940581,SRS3171382,SRP140462,PRJNA450341,Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling,PRJNA450341,Other,Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.,,,MO26h rep1,MO26h 1,Sample3,,strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of fsd1 morphants1,MO26h 1,MO26h 1,RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP140462,,,MO26h_1_1.fq.gz,fastq,1193983450.0,23879669.0,MO26h 1 1.fq.gz,0:50,A:313344068;C:282899939;G:291404437;T:306051122;N:283884,50,,,,313344068,282899939,291404437,306051122,283884,SRX3940581,SRS3171382,SRA690964,"Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology","Institute of Zoology, CHINESE ACADEMY OF SCIENCES",1,0.95658,,0.07921,,0.70307,,0.47586,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-04-16,Pharyngula,Embryo,Trunk,Surface Structure 48055,SRR7008007,SRX3940580,SRS3171381,SRP140462,PRJNA450341,Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling,PRJNA450341,Other,Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.,,,MO26h rep2,MO26h 2,Sample4,,strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of fsd1 morphants2,MO26h 2,MO26h 2,RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP140462,,,MO26h_2_1.fq.gz,fastq,1199524600.0,23990492.0,MO26h 2 1.fq.gz,0:50,A:318726410;C:282721669;G:287606979;T:310182197;N:287345,50,,,,318726410,282721669,287606979,310182197,287345,SRX3940580,SRS3171381,SRA690964,"Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology","Institute of Zoology, CHINESE ACADEMY OF SCIENCES",1,0.9541,,0.08695,,0.70404,,0.47195,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-04-16,Pharyngula,Embryo,Trunk,Surface Structure 48056,SRR7008008,SRX3940579,SRS3171379,SRP140462,PRJNA450341,Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling,PRJNA450341,Other,Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.,,,WT26h rep1,WT26h 1,Sample1,,strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of normal embryos1,WT26h 1,WT26h 1,RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP140462,,,WT26h_1_1.fq.gz,fastq,1200268650.0,24005373.0,WT26h 1 1.fq.gz,0:50,A:315743815;C:284447849;G:295772915;T:303964473;N:339598,50,,,,315743815,284447849,295772915,303964473,339598,SRX3940579,SRS3171379,SRA690964,"Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology","Institute of Zoology, CHINESE ACADEMY OF SCIENCES",1,0.95659,,0.07726,,0.70425,,0.47269,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-04-16,Pharyngula,Embryo,Trunk,Surface Structure 48057,SRR7008009,SRX3940578,SRS3171380,SRP140462,PRJNA450341,Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling,PRJNA450341,Other,Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.,,,WT26h rep2,WT26h 2,Sample2,,strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of normal embryos2,WT26h 2,WT26h 2,RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP140462,,,WT26h_2_1.fq.gz,fastq,1199179850.0,23983597.0,WT26h 2 1.fq.gz,0:50,A:316605984;C:281184572;G:292581373;T:308419476;N:388445,50,,,,316605984,281184572,292581373,308419476,388445,SRX3940578,SRS3171380,SRA690964,"Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology","Institute of Zoology, CHINESE ACADEMY OF SCIENCES",1,0.95377,,0.08617,,0.70508,,0.4775,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-04-16,Pharyngula,Embryo,Trunk,Surface Structure 50717,SRR8257205,SRX5074433,SRS4088243,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 3,GSM3494529,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 3,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494529,GSM3494529: RNAseq in zebrafish wild type embryos at 36hpf replicate 3; Danio rerio; RNA Seq,GSM3494529,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494529,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep3.fq.gz,fastq,2560587500.0,51211750.0,GSM3494529 r1,0:50,A:719232941;C:550474431;G:576590260;T:714289868;N:0,50,,,,719232941,550474431,576590260,714289868,0,SRX5074433,SRS4088243,SRA815839,GEO,CABD/CSIC,1,0.93981,,0.10951,,0.71388,,0.48297,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 50718,SRR8257204,SRX5074432,SRS4088242,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 2,GSM3494528,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 2,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494528,GSM3494528: RNAseq in zebrafish wild type embryos at 36hpf replicate 2; Danio rerio; RNA Seq,GSM3494528,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494528,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep2.fq.gz,fastq,2775840750.0,55516815.0,GSM3494528 r1,0:50,A:783053027;C:587947172;G:603351259;T:801489292;N:0,50,,,,783053027,587947172,603351259,801489292,0,SRX5074432,SRS4088242,SRA815839,GEO,CABD/CSIC,1,0.93386,,0.11853,,0.7007,,0.48856,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 50719,SRR8257203,SRX5074431,SRS4088241,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish wild type embryos at 36hpf replicate 1,GSM3494527,,tissue:whole embryo|developmental stage:36hpf|genotype:WT,RNAseq in zebrafish wild type embryos at 36hpf replicate 1,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:WT,GSM3494527,GSM3494527: RNAseq in zebrafish wild type embryos at 36hpf replicate 1; Danio rerio; RNA Seq,GSM3494527,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_WT_36hpf_rep1.fq.gz,fastq,2638769750.0,52775395.0,GSM3494527 r1,0:50,A:749627286;C:556213831;G:574654547;T:758274086;N:0,50,,,,749627286,556213831,574654547,758274086,0,SRX5074431,SRS4088241,SRA815839,GEO,CABD/CSIC,1,0.92992,,0.12022,,0.72174,,0.49097,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 50720,SRR8257202,SRX5074430,SRS4088240,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3,GSM3494526,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63 / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63 / ,GSM3494526,GSM3494526: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3; Danio rerio; RNA Seq,GSM3494526,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494526,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep3.fq.gz,fastq,2651169450.0,53023389.0,GSM3494526 r1,0:50,A:752539060;C:560162268;G:581624300;T:756843822;N:0,50,,,,752539060,560162268,581624300,756843822,0,SRX5074430,SRS4088240,SRA815839,GEO,CABD/CSIC,1,0.94022,,0.12949,,0.70019,,0.50336,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 50721,SRR8257201,SRX5074429,SRS4088239,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2,GSM3494525,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63 / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63 / ,GSM3494525,GSM3494525: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2; Danio rerio; RNA Seq,GSM3494525,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494525,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep2.fq.gz,fastq,2821501700.0,56430034.0,GSM3494525 r1,0:50,A:795357588;C:599294949;G:620563224;T:806285939;N:0,50,,,,795357588,599294949,620563224,806285939,0,SRX5074429,SRS4088239,SRA815839,GEO,CABD/CSIC,1,0.93671,,0.12314,,0.6957,,0.48362,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 50722,SRR8257200,SRX5074428,SRS4088238,SRP171045,PRJNA507426,Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA seq],GSE123058,Transcriptome Analysis,The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63 knock out mutants that recapitulate human phenotypes and show down regulated epidermal gene expression. Following p63 binding dynamics during development we found two distinct functions clearly separated in space and time. During early development p63 binds enhancers associated to neural genes where it limits Sox3 binding and reduces the expression of these neural genes. Indeed we show that p63 and Sox3 are co expressed in the neural plate border. Later in development p63 binds enhancers associated to epidermal genes and promotes their expression acting as a pioneer factor as it binds to non accessible chromatin and is required for its opening. Therefore our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification promoting the epidermal fate and inhibiting the neural program. Overall design: RNA seq assays in tp63 zebrafish mutants,parent bioproject:PRJNA507423,pubmed:31296872,,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1,GSM3494524,,tissue:whole embryo|developmental stage:36hpf|genotype:tp63 / ,RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1,Reads were aligned against reference genome using STAR software and reads per gene were counted using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were cultivated at 28°C in E3 medium until desired developmental stage,developmental stage:36hpf|genotype:tp63 / ,GSM3494524,GSM3494524: RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1; Danio rerio; RNA Seq,GSM3494524,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM3494524,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP171045,,,RNAseq_zebra_p63mut_36hpf_rep1.fq.gz,fastq,2592494100.0,51849882.0,GSM3494524 r1,0:50,A:730978948;C:550803197;G:572081489;T:738630466;N:0,50,,,,730978948,550803197,572081489,738630466,0,SRX5074428,SRS4088238,SRA815839,GEO,CABD/CSIC,1,0.94035,,0.11571,,0.70796,,0.49468,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2018-11-28,Pharyngula,Embryo,Whole Organism,All anatomical structures 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 52944,SRR9609439,SRX6372833,SRS5033898,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 3,GSM3909672,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909672,GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq,GSM3909672,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909672,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1283013300.0,25660266.0,GSM3909672 r1,0:50,A:339417002;C:304649204;G:297783450;T:341163644;N:0,50,,,,339417002,304649204,297783450,341163644,0,SRX6372833,SRS5033898,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94342,,0.10559,,0.72401,,0.47431,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52945,SRR9609438,SRX6372832,SRS5033897,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 2,GSM3909671,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909671,GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq,GSM3909671,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909671,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1282475700.0,25649514.0,GSM3909671 r1,0:50,A:339635626;C:302447093;G:295507893;T:344885088;N:0,50,,,,339635626,302447093,295507893,344885088,0,SRX6372832,SRS5033897,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94396,,0.10502,,0.71465,,0.47566,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52946,SRR9609437,SRX6372831,SRS5033896,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,PBCAB Replicate 1,GSM3909670,,tissue:Whole Embryo|Stage:12 hpf|treatment:PBCAB,PBCAB Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:PBCAB,GSM3909670,GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq,GSM3909670,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909670,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,PBCAB_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1147572700.0,22951454.0,GSM3909670 r1,0:50,A:300633532;C:273711082;G:268229512;T:304998574;N:0,50,,,,300633532,273711082,268229512,304998574,0,SRX6372831,SRS5033896,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94418,,0.09965,,0.72746,,0.47644,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52947,SRR9609436,SRX6372830,SRS5033895,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 3,GSM3909669,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909669,GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq,GSM3909669,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909669,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1282414400.0,25648288.0,GSM3909669 r1,0:50,A:334687310;C:307161534;G:302070174;T:338495382;N:0,50,,,,334687310,307161534,302070174,338495382,0,SRX6372830,SRS5033895,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94359,,0.09476,,0.72529,,0.47117,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52948,SRR9609435,SRX6372829,SRS5033894,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 2,GSM3909668,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909668,GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq,GSM3909668,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909668,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1281370000.0,25627400.0,GSM3909668 r1,0:50,A:335735118;C:306450529;G:298815464;T:340368889;N:0,50,,,,335735118,306450529,298815464,340368889,0,SRX6372829,SRS5033894,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94338,,0.09412,,0.7204,,0.48662,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52949,SRR9609434,SRX6372828,SRS5033893,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,NF YA DN Replicate 1,GSM3909667,,tissue:Whole Embryo|Stage:12 hpf|treatment:NF YA DN,NF YA DN Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:NF YA DN,GSM3909667,GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq,GSM3909667,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909667,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,NFYADN_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1278504750.0,25570095.0,GSM3909667 r1,0:50,A:334370606;C:306252389;G:299065406;T:338816349;N:0,50,,,,334370606,306252389,299065406,338816349,0,SRX6372828,SRS5033893,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94373,,0.09279,,0.7191,,0.48836,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52950,SRR9609433,SRX6372827,SRS5033892,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 3,GSM3909666,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 3,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909666,GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq,GSM3909666,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909666,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate3.fq.gz,fastq,1284828600.0,25696572.0,GSM3909666 r1,0:50,A:340467505;C:302914392;G:291984238;T:349462465;N:0,50,,,,340467505,302914392,291984238,349462465,0,SRX6372827,SRS5033892,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94288,,0.0963,,0.71713,,0.4793,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52951,SRR9609432,SRX6372826,SRS5033891,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 2,GSM3909665,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 2,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909665,GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq,GSM3909665,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909665,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate2.fq.gz,fastq,1274433150.0,25488663.0,GSM3909665 r1,0:50,A:336050330;C:303141446;G:297353928;T:337887446;N:0,50,,,,336050330,303141446,297353928,337887446,0,SRX6372826,SRS5033891,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94266,,0.0966,,0.72476,,0.47615,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,All anatomical structures 52952,SRR9609431,SRX6372825,SRS5033890,SRP212216,PRJNA551488,TALE and NF Y dependent Genes in 12 hpf Zebrafish Embryos,GSE133459,Transcriptome Analysis,In this RNA seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE PBCAB or NF Y NF YA DN. We normalized each dominant negative condition to GFP. For PBCAB we find 646 downregulated and 854 upregulated genes. For NF YA DN we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription development and homeodomain ontologies while genes downregulated by NF YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF YA DN; these genes are enriched for transcription development and homeodomain ontologies. Overall design: Zebrafish embryos were injected at the 1 cell stage with either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control. Three replicates of 50 100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ 500 platform.,,,,GFP Replicate 1,GSM3909664,,tissue:Whole Embryo|Stage:12 hpf|treatment:GFP,GFP Replicate 1,Sequenced reads were trimmed and rRNA reads were filtered out with Bowtie2. Trimmed and filtered reads were aligned to the GRCz10/danrer10 genome build and the transcripts per million were calculated using RSEM v1.2.28 with parameters p4 bowtie e 70 bowtie chunkmbs 100. PBCAB replicate 2 was excluded as an outlier. Differentially expressed genes were determined using DESeq2. Genome build: GRCz10/danrer10 Supplementary files format and content: TSV files contain transcripts per million TPM values for each sample.,Whole Embryo,Zebrafish embryos at the 1 cell stage were injected with a mixture of mRNA 0.1% phenol red and water. The mRNAs encoded either a dominant negative Pbx PBCAB dominant negative NF YA NF YA DN or GFP control.,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,Injected embryos were raised to 12 hours in egg water 60μg/uL Instant Ocean 0.0002% methylene blue at 29°C.,Stage:12 hpf|treatment:GFP,GSM3909664,GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq,GSM3909664,,1,Embryos were collected in Trizol ThermoFisher Scientific and frozen at 80°C. The samples were then thawed and the embryos were dissociated by pipette. Total RNA was extracted according to the manufacturer's instructions. The extracted RNA was treated with DNase using the RNeasy Column Kit Qiagen and eluted in 30μL of water. Sample quality was assessed on a Bioanalyzer Agilent with all samples having a minimum RNA Quality Number of 8.0 and 28S/18S ratio of 1.0. Library preparation and sequencing were carried out by BGI Inc. Polyadenylated RNAs were selected using oligo dT beads fragmented and reverse transcribed into double stranded cDNAs with N6 random primers. The prepared libraries were then sequenced using the BGISEQ 500 platform.,GEO Accession:GSM3909664,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP212216,,,GFP_12hpf_zebrafish_biological_replicate1.fq.gz,fastq,1278273350.0,25565467.0,GSM3909664 r1,0:50,A:336762127;C:304299745;G:297929933;T:339281545;N:0,50,,,,336762127,304299745,297929933,339281545,0,SRX6372825,SRS5033890,SRA914500,GEO,"Charles Sagerström, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School",1,0.94207,,0.09472,,0.72642,,0.47988,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,bulk,bulk,,United States,2019-06-27,Segmentation,Embryo,Whole Organism,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 57271,SRR12577970,SRX9064853,SRS7314026,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ctrl 3 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 6'|BioSampleModel:Model organism or animal,,,,,,,,,Ctrl 3 zebrafish,Ctrl 3 zebrafish,Ctrl 3 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ctrl_3_1.fq.gz,fastq,1061227250.0,21224545.0,Ctrl 3 1.fq.gz,0:50,A:286099732;C:241244619;G:246876865;T:287006034;N:0,50,,,,286099732,241244619,246876865,287006034,0,SRX9064853,SRS7314026,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94563,,0.10453,,0.70552,,0.46655,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57272,SRR12577971,SRX9064852,SRS7314025,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ctrl 2 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 5 prime|BioSampleModel:Model organism or animal,,,,,,,,,Ctrl 2 zebrafish,Ctrl 2 zebrafish,Ctrl 2 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ctrl_2_1.fq.gz,fastq,1058116700.0,21162334.0,Ctrl 2 1.fq.gz,0:50,A:287223905;C:238707750;G:244987559;T:287197486;N:0,50,,,,287223905,238707750,244987559,287197486,0,SRX9064852,SRS7314025,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94534,,0.11174,,0.70104,,0.47946,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57273,SRR12577972,SRX9064851,SRS7314024,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ctrl 1 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 4'|BioSampleModel:Model organism or animal,,,,,,,,,Ctrl 1 zebrafish,Ctrl 1 zebrafish,Ctrl 1 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ctrl_1_1.fq.gz,fastq,1065919600.0,21318392.0,Ctrl 1 1.fq.gz,0:50,A:295920720;C:242146677;G:242962633;T:284889570;N:0,50,,,,295920720,242146677,242962633,284889570,0,SRX9064851,SRS7314024,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94228,,0.15007,,0.68028,,0.46845,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57274,SRR12577973,SRX9064850,SRS7314023,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator STS 3 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 3 prime|BioSampleModel:Model organism or animal,,,,,,,,,Ator STS 3 zebrafish,Ator STS 3 zebrafish,Ator STS 3 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_STS_3_1.fq.gz,fastq,1059717350.0,21194347.0,Ator STS 3 1.fq.gz,0:50,A:287279590;C:239708340;G:245740313;T:286989107;N:0,50,,,,287279590,239708340,245740313,286989107,0,SRX9064850,SRS7314023,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94345,,0.10458,,0.69686,,0.4755,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57275,SRR12577974,SRX9064849,SRS7314022,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator STS 2 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 2'|BioSampleModel:Model organism or animal,,,,,,,,,Ator STS 2 zebrafish,Ator STS 2 zebrafish,Ator STS 2 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_STS_2_1.fq.gz,fastq,1057950250.0,21159005.0,Ator STS 2 1.fq.gz,0:50,A:286256354;C:238832868;G:244078781;T:288782247;N:0,50,,,,286256354,238832868,244078781,288782247,0,SRX9064849,SRS7314022,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94307,,0.10974,,0.69631,,0.4703,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57276,SRR12577975,SRX9064848,SRS7314021,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator STS 1 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 1'|BioSampleModel:Model organism or animal,,,,,,,,,Ator STS 1 zebrafish,Ator STS 1 zebrafish,Ator STS 1 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_STS_1_1.fq.gz,fastq,1070136700.0,21402734.0,Ator STS 1 1.fq.gz,0:50,A:297601042;C:243837062;G:243583907;T:285114689;N:0,50,,,,297601042,243837062,243583907,285114689,0,SRX9064848,SRS7314021,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94665,,0.12219,,0.67953,,0.46393,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57277,SRR12577976,SRX9064847,SRS7314020,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator 3 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 3 prime|BioSampleModel:Model organism or animal,,,,,,,,,Ator 3 zebrafish,Ator 3 zebrafish,Ator 3 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_3_1.fq.gz,fastq,1058031900.0,21160638.0,Ator 3 1.fq.gz,0:50,A:285399527;C:239993172;G:245571467;T:287067734;N:0,50,,,,285399527,239993172,245571467,287067734,0,SRX9064847,SRS7314020,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94536,,0.11052,,0.6957,,0.48195,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57278,SRR12577977,SRX9064846,SRS7314019,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator 2 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 2'|BioSampleModel:Model organism or animal,,,,,,,,,Ator 2 zebrafish,Ator 2 zebrafish,Ator 2 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_2_1.fq.gz,fastq,1059618400.0,21192368.0,Ator 2 1.fq.gz,0:50,A:283429136;C:243023053;G:248904818;T:284261393;N:0,50,,,,283429136,243023053,248904818,284261393,0,SRX9064846,SRS7314019,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94743,,0.09493,,0.70218,,0.475,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 57279,SRR12577978,SRX9064845,SRS7314018,SRP279881,PRJNA612371,Danio rerio strain:TU Raw sequence reads,PRJNA612371,Whole Genome Sequencing,Hemorrhage stroke is a severe vascular disease of the brain with a high mortality rate in humans. Sodium tanshinone IIA sulfonate STS is a water soluble derivative of tanshinone IIA which is the main active ingredient of Salvia miltiorrhiza Bge known as Danshen in Chinese and has been approved as a commercial drug for treating cardiovascular disease by the China Food and Drug Administration. In our previous study we established a HMG COA inhibitor atorvastatin Ator induced zebrafish model of cerebral hemorrhage and found that STS dramatically decreased both the hemorrhage rate and hemorrhage area although the underlying mechanism was not fully elucidated. Therefore in the present study we conducted transcriptome analysis of the protective effect of STS against Ator induced cerebral hemorrhage in zebrafish using RNA Seq technology and further clarify its underlying molecular mechanisms on HIF 1 and its regulators i.e. the PI3K/Akt and MAPK signaling pathways were verified by real time PCR analysis and specific pharmacological inhibitors. We are also able to show that hemoglobin carbonic anhydrase Na+/H+ exchanger and HIF 1 genes might be potential biomarkers of Ator induced cerebral hemorrhage in zebrafish as well as pharmacological targets of STS. This study also provided evidence of bio markers involved in hemorrhage stroke and improved understanding of the effects of HMG COA inhibition on vascular permeability and cerebral hemorrhage.,,,,,Ator 1 zebrafish,,strain:TU|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:2dpf|dev stage:not collected|sex:not applicable|tissue:head|geo loc name:China:Shanghai|sample type:model organism|replicate:replicate=biological replicate 1'|BioSampleModel:Model organism or animal,,,,,,,,,Ator 1 zebrafish,Ator 1 zebrafish,Ator 1 zebrafish,transcriptome,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,BGISEQ,BGISEQ-500,,SRP279881,,,Ator_1_1.fq.gz,fastq,1075695950.0,21513919.0,Ator 1 1.fq.gz,0:50,A:297768036;C:244470267;G:243768925;T:289688722;N:0,50,,,,297768036,244470267,243768925,289688722,0,SRX9064845,SRS7314018,SRA1120721,Shanghai University of Traditional Chinese Medicine|Longhua Hospital,Shanghai University of Traditional Chinese Medicine,1,0.94468,,0.13183,,0.68363,,0.46288,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2020-09-03,Hatching,Embryo,Head,Nervous System 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 60445,SRR12272862,SRX8777892,SRS7048444,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_2_4.fq,fastq,542610936.0,21965958.0,C2 C2 2 4.fq.gz,0:24.70,A:95221617;C:122628624;G:167025611;T:157730855;N:4229,24,,,,95221617,122628624,167025611,157730855,4229,SRX8777892,SRS7048444,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.8119,,0.10745,,0.85717,,0.51338,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60446,SRR12272863,SRX8777891,SRS7048443,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_1_4.fq,fastq,542847476.0,22614181.0,C2 C2 1 4.fq.gz,0:24.00,A:99999101;C:125407906;G:162383758;T:155055099;N:1612,24,,,,99999101,125407906,162383758,155055099,1612,SRX8777891,SRS7048443,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84327,,0.10491,,0.83256,,0.52046,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60447,SRR12272864,SRX8777890,SRS7048442,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_2_4.fq,fastq,570918284.0,22577002.0,C1 C1 2 4.fq.gz,0:25.29,A:100121235;C:130480588;G:178656113;T:161652765;N:7583,25,,,,100121235,130480588,178656113,161652765,7583,SRX8777890,SRS7048442,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.85096,,0.12542,,0.82873,,0.51535,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60448,SRR12272865,SRX8777889,SRS7048441,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_1_4.fq,fastq,545089417.0,22812164.0,C1 C1 1 4.fq.gz,0:23.89,A:99851844;C:125314095;G:166401335;T:153521167;N:976,23,,,,99851844,125314095,166401335,153521167,976,SRX8777889,SRS7048441,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84602,,0.11725,,0.83159,,0.51353,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60449,SRR12272866,SRX8777888,SRS7048440,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_2_4.fq,fastq,527443144.0,23174740.0,C0 C0 2 4.fq.gz,0:22.76,A:102368401;C:120843229;G:151690193;T:152540806;N:515,22,,,,102368401,120843229,151690193,152540806,515,SRX8777888,SRS7048440,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83063,,0.08114,,0.85169,,0.50894,,16,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60450,SRR12272867,SRX8777887,SRS7048439,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_1_4.fq,fastq,511759408.0,22673361.0,C0 C0 1 4.fq.gz,0:22.57,A:100879182;C:120237907;G:142799495;T:147842595;N:229,22,,,,100879182,120237907,142799495,147842595,229,SRX8777887,SRS7048439,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83904,,0.0823,,0.84741,,0.49929,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60496,SRR12328853,SRX8829078,SRS7048444,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz,fastq fastq,6974294600.0,69742946.0,C2 C2 2 4 1.fq.gz,0:100 1:100,A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0,100,100,,,2057162032,1418016219,1425580374,2073535975,0,SRX8829078,SRS7048444,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93171,,0.17455,,0.71626,,0.54961,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60497,SRR12328854,SRX8829077,SRS7048443,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz,fastq fastq,6942905200.0,69429052.0,C2 C2 1 4 1.fq.gz,0:100 1:100,A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0,100,100,,,2025129308,1433430820,1434784226,2049560846,0,SRX8829077,SRS7048443,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93211,,0.16662,,0.71001,,0.53674,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60498,SRR12328855,SRX8829076,SRS7048442,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz,fastq fastq,6973657600.0,69736576.0,C1 C1 2 4 1.fq.gz,0:100 1:100,A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0,100,100,,,2050440259,1423350359,1423015668,2076851314,0,SRX8829076,SRS7048442,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92911,,0.1877,,0.72025,,0.58085,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60499,SRR12328856,SRX8829075,SRS7048441,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz,fastq fastq,6746729200.0,67467292.0,C1 C1 1 4 1.fq.gz,0:100 1:100,A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0,100,100,,,2004203843,1356765594,1357760526,2027999237,0,SRX8829075,SRS7048441,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92733,,0.19903,,0.72228,,0.59259,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60500,SRR12328857,SRX8829074,SRS7048440,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz,fastq fastq,6924724800.0,69247248.0,C0 C0 2 4 1.fq.gz,0:100 1:100,A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0,100,100,,,1974618038,1471821932,1482725702,1995559128,0,SRX8829074,SRS7048440,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93473,,0.14676,,0.69649,,0.50413,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60501,SRR12328858,SRX8829073,SRS7048439,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz,fastq fastq,6899505600.0,68995056.0,C0 C0 1 4 1.fq.gz,0:100 1:100,A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0,100,100,,,1957459931,1477351919,1482435319,1982258431,0,SRX8829073,SRS7048439,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93567,,0.14057,,0.6883,,0.48707,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60605,SRR12435896,SRX8931591,SRS7187999,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 48hpf replicate 2,GSM4724538,,tissue:whole embryo|developmental stage:48 hpf|genotype:WT,RNA seq in zebrafish wild type embryos at 48hpf replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:WT,GSM4724538,GSM4724538: RNA seq in zebrafish wild type embryos at 48hpf replicate 2; Danio rerio; RNA Seq,GSM4724538,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724538,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_wt_rep2_1.fq.gz,fastq,2857833100.0,57156662.0,GSM4724538 r1,0:50 1:0,A:833205284;C:613960566;G:684040839;T:726626411;N:0,50,0,,,833205284,613960566,684040839,726626411,0,SRX8931591,SRS7187999,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94607,,0.13254,,0.683,,0.47253,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60606,SRR12435895,SRX8931590,SRS7187998,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 48hpf replicate 1,GSM4724537,,tissue:whole embryo|developmental stage:48 hpf|genotype:WT,RNA seq in zebrafish wild type embryos at 48hpf replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:WT,GSM4724537,GSM4724537: RNA seq in zebrafish wild type embryos at 48hpf replicate 1; Danio rerio; RNA Seq,GSM4724537,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724537,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_wt_rep1_1.fq.gz,fastq,1780117200.0,35602344.0,GSM4724537 r1,0:50 1:0,A:515966090;C:381813611;G:432619671;T:449717828;N:0,50,0,,,515966090,381813611,432619671,449717828,0,SRX8931590,SRS7187998,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.95016,,0.1291,,0.68546,,0.47379,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60607,SRR12435894,SRX8931589,SRS7187997,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2,GSM4724536,,tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino,RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino,GSM4724536,GSM4724536: RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 2; Danio rerio; RNA Seq,GSM4724536,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724536,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_wt_p53MO_rep2_1.fq.gz,fastq,1604734300.0,32094686.0,GSM4724536 r1,0:50,A:420858899;C:372944640;G:386038616;T:424892145;N:0,50,,,,420858899,372944640,386038616,424892145,0,SRX8931589,SRS7187997,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.9522,,0.09133,,0.68885,,0.47214,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60608,SRR12435893,SRX8931588,SRS7187996,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1,GSM4724535,,tissue:whole embryo|developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino,RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:WT|treatment:tp53 morpholino,GSM4724535,GSM4724535: RNA seq in zebrafish wild type embryos at 48hpf injected with morpholino against tp53 replicate 1; Danio rerio; RNA Seq,GSM4724535,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724535,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_wt_p53MO_rep1_1.fq.gz,fastq,2384014500.0,47680290.0,GSM4724535 r1,0:50,A:625164876;C:552875690;G:576784849;T:629189085;N:0,50,,,,625164876,552875690,576784849,629189085,0,SRX8931588,SRS7187996,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94749,,0.09167,,0.67978,,0.48327,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60609,SRR12435892,SRX8931587,SRS7187995,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2,GSM4724534,,tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf / ,RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:ctcf / ,GSM4724534,GSM4724534: RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 2; Danio rerio; RNA Seq,GSM4724534,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724534,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_ctcf_rep2_1.fq.gz,fastq,2142745700.0,42854914.0,GSM4724534 r1,0:50 1:0,A:622717093;C:460353664;G:518363295;T:541311648;N:0,50,0,,,622717093,460353664,518363295,541311648,0,SRX8931587,SRS7187995,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94287,,0.14736,,0.69199,,0.47986,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60610,SRR12435891,SRX8931586,SRS7187994,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1,GSM4724533,,tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf / ,RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:ctcf / ,GSM4724533,GSM4724533: RNA seq in zebrafish ctcf mutant embryos at 48hpf replicate 1; Danio rerio; RNA Seq,GSM4724533,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724533,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_ctcf_rep1_1.fq.gz,fastq,1858500400.0,37170008.0,GSM4724533 r1,0:50 1:0,A:544611701;C:398699344;G:449892006;T:465297349;N:0,50,0,,,544611701,398699344,449892006,465297349,0,SRX8931586,SRS7187994,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94363,,0.14349,,0.69089,,0.48114,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60611,SRR12435890,SRX8931585,SRS7187993,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2,GSM4724532,,tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf / |treatment:tp53 morpholino,RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:ctcf / |treatment:tp53 morpholino,GSM4724532,GSM4724532: RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 2; Danio rerio; RNA Seq,GSM4724532,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724532,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_ctcf_p53MO_rep2_1.fq.gz,fastq,2622498950.0,52449979.0,GSM4724532 r1,0:50,A:683425987;C:612438973;G:639683260;T:686950730;N:0,50,,,,683425987,612438973,639683260,686950730,0,SRX8931585,SRS7187993,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94822,,0.10163,,0.69954,,0.4758,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60612,SRR12435889,SRX8931584,SRS7187992,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1,GSM4724531,,tissue:whole embryo|developmental stage:48 hpf|genotype:ctcf / |treatment:tp53 morpholino,RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:48 hpf|genotype:ctcf / |treatment:tp53 morpholino,GSM4724531,GSM4724531: RNA seq in zebrafish ctcf mutant embryos at 48hpf injected with morpholino against tp53 replicate 1; Danio rerio; RNA Seq,GSM4724531,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724531,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_48h_ctcf_p53MO_rep1_1.fq.gz,fastq,2421682100.0,48433642.0,GSM4724531 r1,0:50,A:625808320;C:568572947;G:596940410;T:630360423;N:0,50,,,,625808320,568572947,596940410,630360423,0,SRX8931584,SRS7187992,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94893,,0.09731,,0.71476,,0.48546,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Hatching,Embryo,Whole Organism,All anatomical structures 60613,SRR12435888,SRX8931583,SRS7187991,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 24hpf replicate 2,GSM4724530,,tissue:whole embryo|developmental stage:24 hpf|genotype:WT,RNA seq in zebrafish wild type embryos at 24hpf replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:24 hpf|genotype:WT,GSM4724530,GSM4724530: RNA seq in zebrafish wild type embryos at 24hpf replicate 2; Danio rerio; RNA Seq,GSM4724530,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724530,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_24h_wt_rep2_1.fq.gz,fastq,2241073250.0,44821465.0,GSM4724530 r1,0:50,A:593435654;C:517470954;G:544866646;T:585299996;N:0,50,,,,593435654,517470954,544866646,585299996,0,SRX8931583,SRS7187991,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.9534,,0.07821,,0.70331,,0.47463,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Pharyngula,Embryo,Whole Organism,All anatomical structures 60614,SRR12435887,SRX8931582,SRS7187990,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish wild type embryos at 24hpf replicate 1,GSM4724529,,tissue:whole embryo|developmental stage:24 hpf|genotype:WT,RNA seq in zebrafish wild type embryos at 24hpf replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:24 hpf|genotype:WT,GSM4724529,GSM4724529: RNA seq in zebrafish wild type embryos at 24hpf replicate 1; Danio rerio; RNA Seq,GSM4724529,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724529,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_24h_wt_rep1_1.fq.gz,fastq,1206103900.0,24122078.0,GSM4724529 r1,0:50,A:329983157;C:268788282;G:289794374;T:316858580;N:679507,50,,,,329983157,268788282,289794374,316858580,679507,SRX8931582,SRS7187990,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.94221,,0.09615,,0.69077,,0.47405,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Pharyngula,Embryo,Whole Organism,All anatomical structures 60615,SRR12435886,SRX8931581,SRS7187989,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2,GSM4724528,,tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf / ,RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:24 hpf|genotype:ctcf / ,GSM4724528,GSM4724528: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 2; Danio rerio; RNA Seq,GSM4724528,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724528,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_24h_ctcf_rep2_1.fq.gz,fastq,2823674750.0,56473495.0,GSM4724528 r1,0:50,A:743759446;C:653943934;G:679405104;T:746566266;N:0,50,,,,743759446,653943934,679405104,746566266,0,SRX8931581,SRS7187989,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.95027,,0.08763,,0.6984,,0.487,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Pharyngula,Embryo,Whole Organism,All anatomical structures 60616,SRR12435885,SRX8931580,SRS7187988,SRP277167,PRJNA656771,CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression [RNA seq],GSE156094,Transcriptome Analysis,CTCF is an 11 zinc finger DNA binding protein that acts as a transcriptional repressor and insulator as well as an architectural protein required for 3D genome folding. CTCF mediates long range chromatin looping and is enriched at the boundaries of topologically associating domains TADs which are sub megabase chromatin structures composed of genomic regions with high contact frequency. Although CTCF is essential for cycling cells and developing embryos its in vitro removal has only modest effects over gene expression challenging the generally accepted idea that TADs facilitate enhancer promoter interactions within gene regulatory landscapes. However the effects of an altered CTCF mediated chromatin structure on gene regulation in vivo are poorly understood. Here we have generated a ctcf knockout mutant in zebrafish that allows us to monitor the effect of CTCF loss of function during embryo patterning and organogenesis. CTCF absence leads to a loss of chromatin structure in zebrafish embryos and affects the expression of thousands of genes among them many developmental genes. In addition we show that chromatin accessibility both at CTCF sites and at developmental cis regulatory elements CREs is severely compromised in ctcf mutants. Probing chromatin interactions from developmental genes at high resolution we further demonstrate that promoters fail to fully establish long range contacts with their associated regulatory landscapes leading to altered gene expression patterns during development. Therefore our results demonstrate that CTCF and TADs are essential to finetune gene expression during embryonic development providing the structural basis for the establishment of developmental gene regulatory landscapes. Overall design: RNA seq assays in wild type and ctcf zebrafish mutants at developmental stages 24 hpf and 48 hpf with and without xxx of tp53 morpholino,parent bioproject:PRJNA656767,pubmed:34518536,,RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1,GSM4724527,,tissue:whole embryo|developmental stage:24 hpf|genotype:ctcf / ,RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1,Reads were aligned against reference genome using STAR software Read counts per gene were calculated using htseq count script from HTSeq tools software package Genome build: Zebrafish September 2014 GRCz10/danRer10 Supplementary files format and content: Individual counts files reads per gene,whole embryo,Injection of tp53 morpholino was performed at 1 cell stage,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,Embryos were grown at 28°C in E3 medium until desired developmental stage,developmental stage:24 hpf|genotype:ctcf / ,GSM4724527,GSM4724527: RNA seq in zebrafish ctcf mutant embryos at 24hpf replicate 1; Danio rerio; RNA Seq,GSM4724527,,1,RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen,GEO Accession:GSM4724527,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP277167,,,RNAseq_24h_ctcf_rep1_1.fq.gz,fastq,2408631250.0,48172625.0,GSM4724527 r1,0:50,A:623761639;C:570722378;G:584932664;T:629214569;N:0,50,,,,623761639,570722378,584932664,629214569,0,SRX8931580,SRS7187988,SRA1111981,GEO,"CABD, Universidad Pablo de Olavide-CSIC",1,0.95366,,0.07765,,0.70023,,0.47375,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Spain,2020-08-12,Pharyngula,Embryo,Whole Organism,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 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 71549,SRR21700247,SRX17697774,SRS15228561,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 3,gmfg atgMO 3,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,MO3 20210214,MO3 20210214,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,MO_3_1.fq.gz,fastq,1194263900.0,23885278.0,MO 3 1.fq.gz,0:50 1:0,A:315714579;C:274130504;G:282488713;T:321930104;N:0,50,0,,,315714579,274130504,282488713,321930104,0,SRX17697774,SRS15228561,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.9415,,0.07261,,0.70701,,0.47029,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system 71550,SRR21700248,SRX17697773,SRS15228560,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 2,gmfg atgMO 2,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,MO2 20210213,MO2 20210213,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,MO_2_1.fq.gz,fastq,1193697300.0,23873946.0,MO 2 1.fq.gz,0:50 1:0,A:316188077;C:272941933;G:282559962;T:322007328;N:0,50,0,,,316188077,272941933,282559962,322007328,0,SRX17697773,SRS15228560,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.94144,,0.07426,,0.70715,,0.47856,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system 71551,SRR21700249,SRX17697772,SRS15228559,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 1,gmfg atgMO 1,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:mo1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,MO1 20210212,MO1 20210212,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,MO_1_1.fq.gz,fastq,1194311300.0,23886226.0,MO 1 1.fq.gz,0:50 1:0,A:317344841;C:272348188;G:281111904;T:323506367;N:0,50,0,,,317344841,272348188,281111904,323506367,0,SRX17697772,SRS15228559,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.94366,,0.07701,,0.70274,,0.47929,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system 71552,SRR21700250,SRX17697771,SRS15228558,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 3,ctl 3,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,ctl3 20210211,ctl3 20210211,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,ctl_3_1.fq.gz,fastq,1190502850.0,23810057.0,ctl 3 1.fq.gz,0:50 1:0,A:314168919;C:272277792;G:283249731;T:320806408;N:0,50,0,,,314168919,272277792,283249731,320806408,0,SRX17697771,SRS15228558,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.94354,,0.08493,,0.70228,,0.48147,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system 71553,SRR21700251,SRX17697770,SRS15228557,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 2,ctl 2,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,ctl2 20210210,ctl2 20210210,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,ctl_2_1.fq.gz,fastq,1193941900.0,23878838.0,ctl 2 1.fq.gz,0:50 1:0,A:315521033;C:273947671;G:281554279;T:322918917;N:0,50,0,,,315521033,273947671,281554279,322918917,0,SRX17697770,SRS15228557,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.94073,,0.08514,,0.70281,,0.4767,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system 71554,SRR21700252,SRX17697769,SRS15228556,SRP399479,PRJNA884084,RNA Seq data of gmfg morphants and their control siblings,PRJNA884084,Other,To more specifically explore the underlying mechanism by which gmfg regulates HSPC initiation we performed RNA sequencing RNA Seq with the dissected trunk and tail from 26 hpf gmfg morphants and their control siblings.,,,,biological replicate 1,ctl 1,,strain:not applicable|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:the dissected trunk and tail|collection date:2021 02 26|geo loc name:China:Shenzhen Guangdong|sample type:ctl1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio,ctl1 20210209,ctl1 20210209,RNA seq of Danio rerio in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP399479,,,ctl_1_1.fq.gz,fastq,1194196300.0,23883926.0,ctl 1 1.fq.gz,0:50 1:0,A:315050496;C:273915045;G:282252071;T:322978688;N:0,50,0,,,315050496,273915045,282252071,322978688,0,SRX17697769,SRS15228556,SRA1506658,"the First Affiliated Hospital, School of Medicine, Zhejiang University|BoneMarrow Transplantation Center","the First Affiliated Hospital, School of Medicine, Zhejiang University",1,0.94272,,0.08675,,0.70234,,0.47397,,50,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-09-25,Pharyngula,Embryo,Multi-tissue,Multi-system