{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.platform = \"BGISEQ\" and tissue_curation = \"Whole Organism\"", "rows": [[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", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 3", "GSM3494529", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 719232941, 550474431, 576590260, 714289868, 0, "SRX5074433", "SRS4088243", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93981, null, 0.10951, null, 0.71388, null, 0.48297, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 2", "GSM3494528", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 783053027, 587947172, 603351259, 801489292, 0, "SRX5074432", "SRS4088242", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93386, null, 0.11853, null, 0.7007, null, 0.48856, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNAseq in zebrafish wild type embryos at 36hpf replicate 1", "GSM3494527", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 749627286, 556213831, 574654547, 758274086, 0, "SRX5074431", "SRS4088241", "SRA815839", "GEO", "CABD/CSIC", 1, 0.92992, null, 0.12022, null, 0.72174, null, 0.49097, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 3", "GSM3494526", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 752539060, 560162268, 581624300, 756843822, 0, "SRX5074430", "SRS4088240", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94022, null, 0.12949, null, 0.70019, null, 0.50336, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 2", "GSM3494525", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 795357588, 599294949, 620563224, 806285939, 0, "SRX5074429", "SRS4088239", "SRA815839", "GEO", "CABD/CSIC", 1, 0.93671, null, 0.12314, null, 0.6957, null, 0.48362, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNAseq in zebrafish tp63 mutant embryos at 36hpf replicate 1", "GSM3494524", null, "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", null, "RNA was extracted using TRIsure Bioline and treated with TURBO DNA free kit Invitrogen", "Embryos were cultivated at 28\u00b0C 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", null, "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", null, "SRP171045", null, null, "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, null, null, null, 730978948, 550803197, 572081489, 738630466, 0, "SRX5074428", "SRS4088238", "SRA815839", "GEO", "CABD/CSIC", 1, 0.94035, null, 0.11571, null, 0.70796, null, 0.49468, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2018-11-28", "Pharyngula", "Embryo", "Whole Organism", "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.", null, null, null, "PBCAB Replicate 3", "GSM3909672", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909672", "GSM3909672: PBCAB Replicate 3; Danio rerio; RNA Seq", "GSM3909672", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 339417002, 304649204, 297783450, 341163644, 0, "SRX6372833", "SRS5033898", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94342, null, 0.10559, null, 0.72401, null, 0.47431, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "PBCAB Replicate 2", "GSM3909671", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909671", "GSM3909671: PBCAB Replicate 2; Danio rerio; RNA Seq", "GSM3909671", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 339635626, 302447093, 295507893, 344885088, 0, "SRX6372832", "SRS5033897", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94396, null, 0.10502, null, 0.71465, null, 0.47566, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "PBCAB Replicate 1", "GSM3909670", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:PBCAB", "GSM3909670", "GSM3909670: PBCAB Replicate 1; Danio rerio; RNA Seq", "GSM3909670", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 300633532, 273711082, 268229512, 304998574, 0, "SRX6372831", "SRS5033896", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94418, null, 0.09965, null, 0.72746, null, 0.47644, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "NF YA DN Replicate 3", "GSM3909669", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909669", "GSM3909669: NF YA DN Replicate 3; Danio rerio; RNA Seq", "GSM3909669", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 334687310, 307161534, 302070174, 338495382, 0, "SRX6372830", "SRS5033895", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94359, null, 0.09476, null, 0.72529, null, 0.47117, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "NF YA DN Replicate 2", "GSM3909668", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909668", "GSM3909668: NF YA DN Replicate 2; Danio rerio; RNA Seq", "GSM3909668", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 335735118, 306450529, 298815464, 340368889, 0, "SRX6372829", "SRS5033894", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94338, null, 0.09412, null, 0.7204, null, 0.48662, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "NF YA DN Replicate 1", "GSM3909667", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:NF YA DN", "GSM3909667", "GSM3909667: NF YA DN Replicate 1; Danio rerio; RNA Seq", "GSM3909667", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 334370606, 306252389, 299065406, 338816349, 0, "SRX6372828", "SRS5033893", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94373, null, 0.09279, null, 0.7191, null, 0.48836, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "GFP Replicate 3", "GSM3909666", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909666", "GSM3909666: GFP Replicate 3; Danio rerio; RNA Seq", "GSM3909666", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 340467505, 302914392, 291984238, 349462465, 0, "SRX6372827", "SRS5033892", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94288, null, 0.0963, null, 0.71713, null, 0.4793, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "GFP Replicate 2", "GSM3909665", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909665", "GSM3909665: GFP Replicate 2; Danio rerio; RNA Seq", "GSM3909665", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 336050330, 303141446, 297353928, 337887446, 0, "SRX6372826", "SRS5033891", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94266, null, 0.0966, null, 0.72476, null, 0.47615, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "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.", null, null, null, "GFP Replicate 1", "GSM3909664", null, "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\u00b0C. 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 30\u03bcL 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 60\u03bcg/uL Instant Ocean  0.0002% methylene blue at 29\u00b0C.", "Stage:12 hpf|treatment:GFP", "GSM3909664", "GSM3909664: GFP Replicate 1; Danio rerio; RNA Seq", "GSM3909664", null, "1", "Embryos were collected in Trizol ThermoFisher Scientific and frozen at  80\u00b0C. 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 30\u03bcL 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", null, "SRP212216", null, null, "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, null, null, null, 336762127, 304299745, 297929933, 339281545, 0, "SRX6372825", "SRS5033890", "SRA914500", "GEO", "Charles Sagerstr\u00f6m, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School", 1, 0.94207, null, 0.09472, null, 0.72642, null, 0.47988, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-06-27", "Segmentation", "Embryo", "Whole Organism", "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.", null, null, null, "C2", "C2 C2 2 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2C220200712", "C2C220200712", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.10745, null, 0.85717, null, 0.51338, null, 22, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "C2", "C2 C2 1 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C2C220200711", "C2C220200711", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.10491, null, 0.83256, null, 0.52046, null, 19, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "C1", "C1 C1 2 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1C120200712", "C1C120200712", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.12542, null, 0.82873, null, 0.51535, null, 22, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "C1", "C1 C1 1 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C1C120200711", "C1C120200711", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.11725, null, 0.83159, null, 0.51353, null, 19, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "C0", "C0 C0 2 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0C020200712", "C0C020200712", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.08114, null, 0.85169, null, 0.50894, null, 16, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "C0", "C0 C0 1 4", null, "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", null, null, null, null, null, null, null, null, "RNA seq of zebrafish", "C0C020200711", "C0C020200711", "RNA seq of zebrafish in different conditions", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP272672", null, "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, null, null, null, 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, null, 0.0823, null, 0.84741, null, 0.49929, null, 22, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-08-05", "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", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 2", "GSM4724538", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, 833205284, 613960566, 684040839, 726626411, 0, "SRX8931591", "SRS7187999", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94607, null, 0.13254, null, 0.683, null, 0.47253, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish wild type embryos at 48hpf  replicate 1", "GSM4724537", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, 515966090, 381813611, 432619671, 449717828, 0, "SRX8931590", "SRS7187998", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95016, null, 0.1291, null, 0.68546, null, 0.47379, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724536", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 420858899, 372944640, 386038616, 424892145, 0, "SRX8931589", "SRS7187997", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9522, null, 0.09133, null, 0.68885, null, 0.47214, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish wild type embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724535", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 625164876, 552875690, 576784849, 629189085, 0, "SRX8931588", "SRS7187996", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94749, null, 0.09167, null, 0.67978, null, 0.48327, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 2", "GSM4724534", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, 622717093, 460353664, 518363295, 541311648, 0, "SRX8931587", "SRS7187995", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94287, null, 0.14736, null, 0.69199, null, 0.47986, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  replicate 1", "GSM4724533", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, 544611701, 398699344, 449892006, 465297349, 0, "SRX8931586", "SRS7187994", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94363, null, 0.14349, null, 0.69089, null, 0.48114, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 2", "GSM4724532", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 683425987, 612438973, 639683260, 686950730, 0, "SRX8931585", "SRS7187993", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94822, null, 0.10163, null, 0.69954, null, 0.4758, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 48hpf  injected with morpholino against tp53  replicate 1", "GSM4724531", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 625808320, 568572947, 596940410, 630360423, 0, "SRX8931584", "SRS7187992", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94893, null, 0.09731, null, 0.71476, null, 0.48546, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish wild type embryos at 24hpf  replicate 2", "GSM4724530", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 593435654, 517470954, 544866646, 585299996, 0, "SRX8931583", "SRS7187991", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.9534, null, 0.07821, null, 0.70331, null, 0.47463, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish wild type embryos at 24hpf  replicate 1", "GSM4724529", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 329983157, 268788282, 289794374, 316858580, 679507, "SRX8931582", "SRS7187990", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.94221, null, 0.09615, null, 0.69077, null, 0.47405, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 2", "GSM4724528", null, "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\u00b0C 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", null, "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", null, "SRP277167", null, null, "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, null, null, null, 743759446, 653943934, 679405104, 746566266, 0, "SRX8931581", "SRS7187989", "SRA1111981", "GEO", "CABD, Universidad Pablo de Olavide-CSIC", 1, 0.95027, null, 0.08763, null, 0.6984, null, 0.487, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "RNA seq in zebrafish ctcf mutant embryos at 24hpf  replicate 1", "GSM4724527", null, "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\u00b0C in E3 medium until desired developmental stage", "developmental 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