{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_strategy = \"OTHER\", technology = \"unknown\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[33990, "SRR31030860", "SRX26416598", "SRS22936450", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep4 minus", "GSM8578751", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578751", "GSM8578751: ZF NES GAPDH Rep4 minus; Danio rerio; OTHER", "GSM8578751 r1", "GSM8578751", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep4_minus.R1.fq.gz ZF_NES_GAPDH_Rep4_minus.R2.fq.gz", "fastq fastq", 1100578200.0, 3668594.0, "GSM8578751 r1", "0:150 1:150", "A:287878221;C:249390946;G:265835736;T:297454600;N:18697", 150, 150, null, null, 287878221, 249390946, 265835736, 297454600, 18697, "SRX26416598", "SRS22936450", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33991, "SRR31030861", "SRX26416597", "SRS22936451", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 plus", "GSM8578750", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578750", "GSM8578750: ZF NES GAPDH Rep3 plus; Danio rerio; OTHER", "GSM8578750 r1", "GSM8578750", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 minus", "GSM8578749", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578749", "GSM8578749: ZF NES GAPDH Rep3 minus; Danio rerio; OTHER", "GSM8578749 r1", "GSM8578749", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 plus", "GSM8578748", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 minus", "GSM8578747", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 plus", "GSM8578746", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 minus", "GSM8578745", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep1_minus.R1.fq.gz ZF_NES_GAPDH_Rep1_minus.R2.fq.gz", "fastq fastq", 911747100.0, 3039157.0, "GSM8578745 r1", "0:150 1:150", "A:239833349;C:205185786;G:218897710;T:247814511;N:15744", 150, 150, null, null, 239833349, 205185786, 218897710, 247814511, 15744, "SRX26416592", "SRS22936445", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33997, "SRR31030867", "SRX26416591", "SRS22936444", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 plus", "GSM8578744", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep4 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578744", "GSM8578744: ZF H2B MALAT1 Rep4 plus; Danio rerio; OTHER", "GSM8578744 r1", "GSM8578744", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep4_plus.R1.fq.gz ZF_H2B_MALAT1_Rep4_plus.R2.fq.gz", "fastq fastq", 842103300.0, 2807011.0, "GSM8578744 r1", "0:150 1:150", "A:204870477;C:222752099;G:215404135;T:199062275;N:14314", 150, 150, null, null, 204870477, 222752099, 215404135, 199062275, 14314, "SRX26416591", "SRS22936444", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33998, "SRR31030868", "SRX26416590", "SRS22936442", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 minus", "GSM8578743", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578743", "GSM8578743: ZF H2B MALAT1 Rep4 minus; Danio rerio; OTHER", "GSM8578743 r1", "GSM8578743", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep4_minus.R1.fq.gz ZF_H2B_MALAT1_Rep4_minus.R2.fq.gz", "fastq fastq", 1166375100.0, 3887917.0, "GSM8578743 r1", "0:150 1:150", "A:283781955;C:308660466;G:298298204;T:275614377;N:20098", 150, 150, null, null, 283781955, 308660466, 298298204, 275614377, 20098, "SRX26416590", "SRS22936442", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33999, "SRR31030869", "SRX26416589", "SRS22936443", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 plus", "GSM8578742", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578742", "GSM8578742: ZF H2B MALAT1 Rep3 plus; Danio rerio; OTHER", "GSM8578742 r1", "GSM8578742", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep3_plus.R1.fq.gz ZF_H2B_MALAT1_Rep3_plus.R2.fq.gz", "fastq fastq", 1159439400.0, 3864798.0, "GSM8578742 r1", "0:150 1:150", "A:282055391;C:306842216;G:296569227;T:273952570;N:19996", 150, 150, null, null, 282055391, 306842216, 296569227, 273952570, 19996, "SRX26416589", "SRS22936443", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34000, "SRR31030870", "SRX26416588", "SRS22936440", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 minus", "GSM8578741", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578741", "GSM8578741: ZF H2B MALAT1 Rep3 minus; Danio rerio; OTHER", "GSM8578741 r1", "GSM8578741", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep3_minus.R1.fq.gz ZF_H2B_MALAT1_Rep3_minus.R2.fq.gz", "fastq fastq", 1008297600.0, 3360992.0, "GSM8578741 r1", "0:150 1:150", "A:245277585;C:266840408;G:257911846;T:238251305;N:16456", 150, 150, null, null, 245277585, 266840408, 257911846, 238251305, 16456, "SRX26416588", "SRS22936440", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34001, "SRR31030871", "SRX26416587", "SRS22936441", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 plus", "GSM8578740", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578740", "GSM8578740: ZF H2B MALAT1 Rep2 plus; Danio rerio; OTHER", "GSM8578740 r1", "GSM8578740", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep2_plus.R1.fq.gz ZF_H2B_MALAT1_Rep2_plus.R2.fq.gz", "fastq fastq", 1419263400.0, 4730878.0, "GSM8578740 r1", "0:150 1:150", "A:345302268;C:375591885;G:362956395;T:335387828;N:25024", 150, 150, null, null, 345302268, 375591885, 362956395, 335387828, 25024, "SRX26416587", "SRS22936441", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34002, "SRR31030872", "SRX26416586", "SRS22936439", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 minus", "GSM8578739", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578739", "GSM8578739: ZF H2B MALAT1 Rep2 minus; Danio rerio; OTHER", "GSM8578739 r1", "GSM8578739", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep2_minus.R1.fq.gz ZF_H2B_MALAT1_Rep2_minus.R2.fq.gz", "fastq fastq", 1249910700.0, 4166369.0, "GSM8578739 r1", "0:150 1:150", "A:304074828;C:330741431;G:319677748;T:295395235;N:21458", 150, 150, null, null, 304074828, 330741431, 319677748, 295395235, 21458, "SRX26416586", "SRS22936439", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34003, "SRR31030873", "SRX26416585", "SRS22936438", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 plus", "GSM8578738", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578738", "GSM8578738: ZF H2B MALAT1 Rep1 plus; Danio rerio; OTHER", "GSM8578738 r1", "GSM8578738", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep1_plus.R1.fq.gz ZF_H2B_MALAT1_Rep1_plus.R2.fq.gz", "fastq fastq", 1257872700.0, 4192909.0, "GSM8578738 r1", "0:150 1:150", "A:306022947;C:332851039;G:321699513;T:297277788;N:21413", 150, 150, null, null, 306022947, 332851039, 321699513, 297277788, 21413, "SRX26416585", "SRS22936438", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34004, "SRR31030874", "SRX26416584", "SRS22936437", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 minus", "GSM8578737", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578737", "GSM8578737: ZF H2B MALAT1 Rep1 minus; Danio rerio; OTHER", "GSM8578737 r1", "GSM8578737", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep1_minus.R1.fq.gz ZF_H2B_MALAT1_Rep1_minus.R2.fq.gz", "fastq fastq", 1377040200.0, 4590134.0, "GSM8578737 r1", "0:150 1:150", "A:335021330;C:364359707;G:352178356;T:325457746;N:23061", 150, 150, null, null, 335021330, 364359707, 352178356, 325457746, 23061, "SRX26416584", "SRS22936437", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34005, "SRR31030875", "SRX26416583", "SRS22936435", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep4 plus", "GSM8578736", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep4 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578736", "GSM8578736: ZF H2B GAPDH Rep4 plus; Danio rerio; OTHER", "GSM8578736 r1", "GSM8578736", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep4_plus.R1.fq.gz ZF_H2B_GAPDH_Rep4_plus.R2.fq.gz", "fastq fastq", 1051103100.0, 3503677.0, "GSM8578736 r1", "0:150 1:150", "A:274220771;C:238733668;G:254670769;T:283460283;N:17609", 150, 150, null, null, 274220771, 238733668, 254670769, 283460283, 17609, "SRX26416583", "SRS22936435", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34006, "SRR31030876", "SRX26416582", "SRS22936436", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep4 minus", "GSM8578735", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578735", "GSM8578735: ZF H2B GAPDH Rep4 minus; Danio rerio; OTHER", "GSM8578735 r1", "GSM8578735", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep4_minus.R1.fq.gz ZF_H2B_GAPDH_Rep4_minus.R2.fq.gz", "fastq fastq", 1206485700.0, 4021619.0, "GSM8578735 r1", "0:150 1:150", "A:314740194;C:274101014;G:292357972;T:325267132;N:19388", 150, 150, null, null, 314740194, 274101014, 292357972, 325267132, 19388, "SRX26416582", "SRS22936436", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34007, "SRR31030877", "SRX26416581", "SRS22936434", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep3 plus", "GSM8578734", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578734", "GSM8578734: ZF H2B GAPDH Rep3 plus; Danio rerio; OTHER", "GSM8578734 r1", "GSM8578734", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep3_plus.R1.fq.gz ZF_H2B_GAPDH_Rep3_plus.R2.fq.gz", "fastq fastq", 1140550200.0, 3801834.0, "GSM8578734 r1", "0:150 1:150", "A:297636297;C:258828826;G:276373993;T:307692213;N:18871", 150, 150, null, null, 297636297, 258828826, 276373993, 307692213, 18871, "SRX26416581", "SRS22936434", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34008, "SRR31030878", "SRX26416580", "SRS22936433", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep3 minus", "GSM8578733", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578733", "GSM8578733: ZF H2B GAPDH Rep3 minus; Danio rerio; OTHER", "GSM8578733 r1", "GSM8578733", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep3_minus.R1.fq.gz ZF_H2B_GAPDH_Rep3_minus.R2.fq.gz", "fastq fastq", 782406600.0, 2608022.0, "GSM8578733 r1", "0:150 1:150", "A:204132316;C:177696721;G:189675433;T:210888939;N:13191", 150, 150, null, null, 204132316, 177696721, 189675433, 210888939, 13191, "SRX26416580", "SRS22936433", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34009, "SRR31030879", "SRX26416579", "SRS22936431", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep2 plus", "GSM8578732", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578732", "GSM8578732: ZF H2B GAPDH Rep2 plus; Danio rerio; OTHER", "GSM8578732 r1", "GSM8578732", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep2_plus.R1.fq.gz ZF_H2B_GAPDH_Rep2_plus.R2.fq.gz", "fastq fastq", 958297200.0, 3194324.0, "GSM8578732 r1", "0:150 1:150", "A:250011335;C:217600823;G:232206339;T:258462392;N:16311", 150, 150, null, null, 250011335, 217600823, 232206339, 258462392, 16311, "SRX26416579", "SRS22936431", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34010, "SRR31030880", "SRX26416578", "SRS22936432", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep2 minus", "GSM8578731", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578731", "GSM8578731: ZF H2B GAPDH Rep2 minus; Danio rerio; OTHER", "GSM8578731 r1", "GSM8578731", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep2_minus.R1.fq.gz ZF_H2B_GAPDH_Rep2_minus.R2.fq.gz", "fastq fastq", 1020926700.0, 3403089.0, "GSM8578731 r1", "0:150 1:150", "A:266429488;C:231749424;G:247353147;T:275377720;N:16921", 150, 150, null, null, 266429488, 231749424, 247353147, 275377720, 16921, "SRX26416578", "SRS22936432", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34011, "SRR31030881", "SRX26416577", "SRS22936430", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep1 plus", "GSM8578730", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578730", "GSM8578730: ZF H2B GAPDH Rep1 plus; Danio rerio; OTHER", "GSM8578730 r1", "GSM8578730", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep1_plus.R1.fq.gz ZF_H2B_GAPDH_Rep1_plus.R2.fq.gz", "fastq fastq", 1134318600.0, 3781062.0, "GSM8578730 r1", "0:150 1:150", "A:295931335;C:257596481;G:274848790;T:305922827;N:19167", 150, 150, null, null, 295931335, 257596481, 274848790, 305922827, 19167, "SRX26416577", "SRS22936430", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34012, "SRR31030882", "SRX26416576", "SRS22936429", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep1 minus", "GSM8578729", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578729", "GSM8578729: ZF H2B GAPDH Rep1 minus; Danio rerio; OTHER", "GSM8578729 r1", "GSM8578729", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_GAPDH_Rep1_minus.R1.fq.gz ZF_H2B_GAPDH_Rep1_minus.R2.fq.gz", "fastq fastq", 752638800.0, 2508796.0, "GSM8578729 r1", "0:150 1:150", "A:196331185;C:170899863;G:182460258;T:202935049;N:12445", 150, 150, null, null, 196331185, 170899863, 182460258, 202935049, 12445, "SRX26416576", "SRS22936429", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate1-mate2 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34013, "SRR31031004", "SRX26416454", "SRS22936307", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep3", "GSM8578770", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing", "Zeb WT pDBF Rep3", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF", "GSM8578770", "GSM8578770: Zeb WT pDBF Rep3; Danio rerio; OTHER", "GSM8578770 r1", "GSM8578770", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_pDBF_Rep3.R1.fq.gz Zeb_WT_pDBF_Rep3.R2.fq.gz", "fastq fastq", 23216831100.0, 77389437.0, "GSM8578770 r1", "0:150 1:150", "A:7577896837;C:3508911439;G:4823311862;T:7306393244;N:317718", 150, 150, null, null, 7577896837, 3508911439, 4823311862, 7306393244, 317718, "SRX26416454", "SRS22936307", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34014, "SRR31031005", "SRX26416453", "SRS22936305", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep2", "GSM8578769", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing", "Zeb WT pDBF Rep2", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF", "GSM8578769", "GSM8578769: Zeb WT pDBF Rep2; Danio rerio; OTHER", "GSM8578769 r1", "GSM8578769", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_pDBF_Rep2.R1.fq.gz Zeb_WT_pDBF_Rep2.R2.fq.gz", "fastq fastq", 27237049500.0, 90790165.0, "GSM8578769 r1", "0:150 1:150", "A:8800724632;C:4062692793;G:5651432074;T:8721823175;N:376826", 150, 150, null, null, 8800724632, 4062692793, 5651432074, 8721823175, 376826, "SRX26416453", "SRS22936305", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34015, "SRR31031006", "SRX26416452", "SRS22936306", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT pDBF Rep1", "GSM8578768", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF|geo loc name:missing|collection date:missing", "Zeb WT pDBF Rep1", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:plus DBF", "GSM8578768", "GSM8578768: Zeb WT pDBF Rep1; Danio rerio; OTHER", "GSM8578768 r1", "GSM8578768", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_pDBF_Rep1.R1.fq.gz Zeb_WT_pDBF_Rep1.R2.fq.gz", "fastq fastq", 22364115300.0, 74547051.0, "GSM8578768 r1", "0:150 1:150", "A:7336106577;C:3346831944;G:4451536371;T:7229335436;N:304972", 150, 150, null, null, 7336106577, 3346831944, 4451536371, 7229335436, 304972, "SRX26416452", "SRS22936306", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34016, "SRR31031007", "SRX26416451", "SRS22936304", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep3", "GSM8578767", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing", "Zeb WT mDBF Rep3", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF", "GSM8578767", "GSM8578767: Zeb WT mDBF Rep3; Danio rerio; OTHER", "GSM8578767 r1", "GSM8578767", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_mDBF_Rep3.R1.fq.gz Zeb_WT_mDBF_Rep3.R2.fq.gz", "fastq fastq", 20112719100.0, 67042397.0, "GSM8578767 r1", "0:150 1:150", "A:6537370232;C:2924919118;G:3973928235;T:6676228153;N:273362", 150, 150, null, null, 6537370232, 2924919118, 3973928235, 6676228153, 273362, "SRX26416451", "SRS22936304", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34017, "SRR31031008", "SRX26416450", "SRS22936303", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep2", "GSM8578766", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing", "Zeb WT mDBF Rep2", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF", "GSM8578766", "GSM8578766: Zeb WT mDBF Rep2; Danio rerio; OTHER", "GSM8578766 r1", "GSM8578766", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_mDBF_Rep2.R1.fq.gz Zeb_WT_mDBF_Rep2.R2.fq.gz", "fastq fastq", 24839552100.0, 82798507.0, "GSM8578766 r1", "0:150 1:150", "A:8176074473;C:3715794630;G:4984816273;T:7962528150;N:338574", 150, 150, null, null, 8176074473, 3715794630, 4984816273, 7962528150, 338574, "SRX26416450", "SRS22936303", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34018, "SRR31031009", "SRX26416449", "SRS22936302", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb WT mDBF Rep1", "GSM8578765", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF|geo loc name:missing|collection date:missing", "Zeb WT mDBF Rep1", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:wildtype|treatment:minus DBF", "GSM8578765", "GSM8578765: Zeb WT mDBF Rep1; Danio rerio; OTHER", "GSM8578765 r1", "GSM8578765", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_WT_mDBF_Rep1.R1.fq.gz Zeb_WT_mDBF_Rep1.R2.fq.gz", "fastq fastq", 23029785600.0, 76765952.0, "GSM8578765 r1", "0:150 1:150", "A:7509388471;C:3438475939;G:4820328116;T:7261277960;N:315114", 150, 150, null, null, 7509388471, 3438475939, 4820328116, 7261277960, 315114, "SRX26416449", "SRS22936302", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34019, "SRR31031010", "SRX26416448", "SRS22936301", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES pDBF Rep2", "GSM8578764", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "Zeb NES pDBF Rep2", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578764", "GSM8578764: Zeb NES pDBF Rep2; Danio rerio; OTHER", "GSM8578764 r1", "GSM8578764", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_NES_pDBF_Rep2.R1.fq.gz Zeb_NES_pDBF_Rep2.R2.fq.gz", "fastq fastq", 25465584900.0, 84885283.0, "GSM8578764 r1", "0:150 1:150", "A:7944190976;C:4330095891;G:5473069331;T:7718120992;N:107710", 150, 150, null, null, 7944190976, 4330095891, 5473069331, 7718120992, 107710, "SRX26416448", "SRS22936301", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34020, "SRR31031011", "SRX26416447", "SRS22936300", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES pDBF Rep1", "GSM8578763", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "Zeb NES pDBF Rep1", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578763", "GSM8578763: Zeb NES pDBF Rep1; Danio rerio; OTHER", "GSM8578763 r1", "GSM8578763", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_NES_pDBF_Rep1.R1.fq.gz Zeb_NES_pDBF_Rep1.R2.fq.gz", "fastq fastq", 21107351400.0, 70357838.0, "GSM8578763 r1", "0:150 1:150", "A:6528579219;C:3620666961;G:4496642830;T:6461373643;N:88747", 150, 150, null, null, 6528579219, 3620666961, 4496642830, 6461373643, 88747, "SRX26416447", "SRS22936300", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34021, "SRR31031012", "SRX26416446", "SRS22936299", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES mDBF Rep2", "GSM8578762", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "Zeb NES mDBF Rep2", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578762", "GSM8578762: Zeb NES mDBF Rep2; Danio rerio; OTHER", "GSM8578762 r1", "GSM8578762", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_NES_mDBF_Rep2.R1.fq.gz Zeb_NES_mDBF_Rep2.R2.fq.gz", "fastq fastq", 21542967300.0, 71809891.0, "GSM8578762 r1", "0:150 1:150", "A:6722613760;C:3654507931;G:4628076548;T:6537678084;N:90977", 150, 150, null, null, 6722613760, 3654507931, 4628076548, 6537678084, 90977, "SRX26416446", "SRS22936299", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34022, "SRR31031013", "SRX26416445", "SRS22936297", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "Zeb NES mDBF Rep1", "GSM8578761", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "Zeb NES mDBF Rep1", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578761", "GSM8578761: Zeb NES mDBF Rep1; Danio rerio; OTHER", "GSM8578761 r1", "GSM8578761", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "Zeb_NES_mDBF_Rep1.R1.fq.gz Zeb_NES_mDBF_Rep1.R2.fq.gz", "fastq fastq", 23038870800.0, 76796236.0, "GSM8578761 r1", "0:150 1:150", "A:7216059153;C:3815899397;G:4909028200;T:7097787584;N:96466", 150, 150, null, null, 7216059153, 3815899397, 4909028200, 7097787584, 96466, "SRX26416445", "SRS22936297", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34023, "SRR31031014", "SRX26416444", "SRS22936298", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep4 plus", "GSM8578760", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep4 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578760", "GSM8578760: ZF NES MALAT1 Rep4 plus; Danio rerio; OTHER", "GSM8578760 r1", "GSM8578760", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep4_plus.R1.fq.gz ZF_NES_MALAT1_Rep4_plus.R2.fq.gz", "fastq fastq", 1091293200.0, 3637644.0, "GSM8578760 r1", "0:150 1:150", "A:265519561;C:288647650;G:279105515;T:258001510;N:18964", 150, 150, null, null, 265519561, 288647650, 279105515, 258001510, 18964, "SRX26416444", "SRS22936298", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34024, "SRR31031015", "SRX26416443", "SRS22936296", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep4 minus", "GSM8578759", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578759", "GSM8578759: ZF NES MALAT1 Rep4 minus; Danio rerio; OTHER", "GSM8578759 r1", "GSM8578759", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep4_minus.R1.fq.gz ZF_NES_MALAT1_Rep4_minus.R2.fq.gz", "fastq fastq", 1395963600.0, 4653212.0, "GSM8578759 r1", "0:150 1:150", "A:339654289;C:369433701;G:356957685;T:329893853;N:24072", 150, 150, null, null, 339654289, 369433701, 356957685, 329893853, 24072, "SRX26416443", "SRS22936296", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34025, "SRR31031016", "SRX26416442", "SRS22936295", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep3 plus", "GSM8578758", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578758", "GSM8578758: ZF NES MALAT1 Rep3 plus; Danio rerio; OTHER", "GSM8578758 r1", "GSM8578758", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep3_plus.R1.fq.gz ZF_NES_MALAT1_Rep3_plus.R2.fq.gz", "fastq fastq", 1556195100.0, 5187317.0, "GSM8578758 r1", "0:150 1:150", "A:378553535;C:411730281;G:398086882;T:367797563;N:26839", 150, 150, null, null, 378553535, 411730281, 398086882, 367797563, 26839, "SRX26416442", "SRS22936295", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34026, "SRR31031017", "SRX26416441", "SRS22936294", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep3 minus", "GSM8578757", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578757", "GSM8578757: ZF NES MALAT1 Rep3 minus; Danio rerio; OTHER", "GSM8578757 r1", "GSM8578757", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep3_minus.R1.fq.gz ZF_NES_MALAT1_Rep3_minus.R2.fq.gz", "fastq fastq", 1511328900.0, 5037763.0, "GSM8578757 r1", "0:150 1:150", "A:367639521;C:400036694;G:386523395;T:357103340;N:25950", 150, 150, null, null, 367639521, 400036694, 386523395, 357103340, 25950, "SRX26416441", "SRS22936294", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34027, "SRR31031018", "SRX26416440", "SRS22936293", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep2 plus", "GSM8578756", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578756", "GSM8578756: ZF NES MALAT1 Rep2 plus; Danio rerio; OTHER", "GSM8578756 r1", "GSM8578756", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep2_plus.R1.fq.gz ZF_NES_MALAT1_Rep2_plus.R2.fq.gz", "fastq fastq", 1451137800.0, 4837126.0, "GSM8578756 r1", "0:150 1:150", "A:353052445;C:383981771;G:371154128;T:342925275;N:24181", 150, 150, null, null, 353052445, 383981771, 371154128, 342925275, 24181, "SRX26416440", "SRS22936293", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34028, "SRR31031019", "SRX26416439", "SRS22936292", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep2 minus", "GSM8578755", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578755", "GSM8578755: ZF NES MALAT1 Rep2 minus; Danio rerio; OTHER", "GSM8578755 r1", "GSM8578755", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep2_minus.R1.fq.gz ZF_NES_MALAT1_Rep2_minus.R2.fq.gz", "fastq fastq", 1286489400.0, 4288298.0, "GSM8578755 r1", "0:150 1:150", "A:312986127;C:340482608;G:329001591;T:303997982;N:21092", 150, 150, null, null, 312986127, 340482608, 329001591, 303997982, 21092, "SRX26416439", "SRS22936292", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34029, "SRR31031020", "SRX26416438", "SRS22936291", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep1 plus", "GSM8578754", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578754", "GSM8578754: ZF NES MALAT1 Rep1 plus; Danio rerio; OTHER", "GSM8578754 r1", "GSM8578754", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep1_plus.R1.fq.gz ZF_NES_MALAT1_Rep1_plus.R2.fq.gz", "fastq fastq", 1146380100.0, 3821267.0, "GSM8578754 r1", "0:150 1:150", "A:278826422;C:303464534;G:293239572;T:270830265;N:19307", 150, 150, null, null, 278826422, 303464534, 293239572, 270830265, 19307, "SRX26416438", "SRS22936291", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34030, "SRR31031021", "SRX26416437", "SRS22936289", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES MALAT1 Rep1 minus", "GSM8578753", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES MALAT1 Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578753", "GSM8578753: ZF NES MALAT1 Rep1 minus; Danio rerio; OTHER", "GSM8578753 r1", "GSM8578753", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_MALAT1_Rep1_minus.R1.fq.gz ZF_NES_MALAT1_Rep1_minus.R2.fq.gz", "fastq fastq", 1149087000.0, 3830290.0, "GSM8578753 r1", "0:150 1:150", "A:279487473;C:304130198;G:293947979;T:271501018;N:20332", 150, 150, null, null, 279487473, 304130198, 293947979, 271501018, 20332, "SRX26416437", "SRS22936289", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34031, "SRR31031022", "SRX26416436", "SRS22936290", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep4 plus", "GSM8578752", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep4 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578752", "GSM8578752: ZF NES GAPDH Rep4 plus; Danio rerio; OTHER", "GSM8578752 r1", "GSM8578752", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. 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CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo prim20 stage", "D. rerio prim20 embryo", "D. rerio prim20 embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio prim20 embryo", "CAGE   D. rerio prim20 embryo run2", "D. rerio prim20 embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_prim20_run1.fastq", "fastq", 76770666.0, 2843358.0, "CAGE   D. rerio prim20 embryo run1", "0:27", "A:19320047;C:17585086;G:22511175;T:17354358;N:0", 27, null, null, null, 19320047, 17585086, 22511175, 17354358, 0, "SRX156356", "SRS347213", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.56472, null, 0.10044, null, 0.77469, null, 0.74192, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36410, "SRR516561", "SRX156356", "SRS347213", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. 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Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo prim6 stage", "D. rerio prim6 embryo", "D. rerio prim6 embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio prim6 embryo", "CAGE   D. rerio prim6 embryo", "D. rerio prim6 embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_prim6.fastq", "fastq", 283414275.0, 10496825.0, "CAGE   D. rerio prim6 embryo", "0:27", "A:70974303;C:66202040;G:80064124;T:66173808;N:0", 27, null, null, null, 70974303, 66202040, 80064124, 66173808, 0, "SRX156355", "SRS347212", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.53395, null, 0.07806, null, 0.78255, null, 0.77575, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2013-08-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36412, "SRR516557", "SRX156352", "SRS347211", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 14 somites stage", "D. rerio 14 somites embryo", "D. rerio 14 somites embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 14 somites embryo", "CAGE   D. rerio 14 somites embryo run2", "D. rerio 14 somites embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 73689048.0, 2729224.0, "CAGE   D. rerio 14 somites embryo run1", "0:27", "A:19506796;C:16238588;G:21636330;T:16307334;N:0", 27, null, null, null, 19506796, 16238588, 21636330, 16307334, 0, "SRX156352", "SRS347211", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.63348, null, 0.09461, null, 0.76199, null, 0.68697, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36413, "SRR516558", "SRX156352", "SRS347211", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 14 somites stage", "D. rerio 14 somites embryo", "D. rerio 14 somites embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 14 somites embryo", "CAGE   D. rerio 14 somites embryo run2", "D. rerio 14 somites embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_14somites_run2.fastq", "fastq", 212381811.0, 7865993.0, "CAGE   D. rerio 14 somites embryo run2", "0:27", "A:53780820;C:47467464;G:59893810;T:51239717;N:0", 27, null, null, null, 53780820, 47467464, 59893810, 51239717, 0, "SRX156352", "SRS347211", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.5278, null, 0.0806, null, 0.77589, null, 0.72881, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36414, "SRR516555", "SRX156350", "SRS347210", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo shield stage", "D. rerio shield embryo", "D. rerio shield embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio shield embryo", "CAGE   D. rerio shield embryo run2", "D. rerio shield embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 81086886.0, 3003218.0, "CAGE   D. rerio shield embryo run1", "0:27", "A:20800196;C:18582826;G:23491216;T:18212648;N:0", 27, null, null, null, 20800196, 18582826, 23491216, 18212648, 0, "SRX156350", "SRS347210", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.60434, null, 0.09948, null, 0.80432, null, 0.72631, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36415, "SRR516556", "SRX156350", "SRS347210", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. 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CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo shield stage", "D. rerio shield embryo", "D. rerio shield embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio shield embryo", "CAGE   D. rerio shield embryo run2", "D. rerio shield embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_shield_run2.fastq", "fastq", 81675891.0, 3025033.0, "CAGE   D. rerio shield embryo run2", "0:27", "A:21590166;C:17662459;G:22692127;T:19731139;N:0", 27, null, null, null, 21590166, 17662459, 22692127, 19731139, 0, "SRX156350", "SRS347210", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.52624, null, 0.08062, null, 0.81793, null, 0.76291, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36416, "SRR516554", "SRX156349", "SRS347209", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. 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CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo dome/zfs:0000015 stage", "D. rerio dome/zfs:0000015 embryo", "D. rerio dome/zfs:0000015 embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio dome/zfs:0000015 embryo", "CAGE   D. rerio dome/zfs:0000015 embryo", "D. rerio dome/zfs:0000015 embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_30p_dome.fastq", "fastq", 165690819.0, 6136697.0, "CAGE   D. rerio dome/zfs:0000015 embryo", "0:27", "A:42721293;C:36492232;G:46154926;T:40322368;N:0", 27, null, null, null, 42721293, 36492232, 46154926, 40322368, 0, "SRX156349", "SRS347209", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.50236, null, 0.0905, null, 0.81824, null, 0.8156, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36417, "SRR516552", "SRX156347", "SRS347208", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. 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CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo sphere/dome stage", "D. rerio sphere/dome embryo", "D. rerio sphere/dome embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio sphere/dome embryo", "CAGE   D. rerio sphere/dome embryo run2", "D. rerio sphere/dome embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_sphere_dome_run1.fastq", "fastq", 78937740.0, 2923620.0, "CAGE   D. rerio sphere/dome embryo run1", "0:27", "A:20705496;C:17020957;G:22237043;T:18974244;N:0", 27, null, null, null, 20705496, 17020957, 22237043, 18974244, 0, "SRX156347", "SRS347208", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.50917, null, 0.09193, null, 0.81523, null, 0.8084, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36418, "SRR516553", "SRX156347", "SRS347208", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo sphere/dome stage", "D. rerio sphere/dome embryo", "D. rerio sphere/dome embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio sphere/dome embryo", "CAGE   D. rerio sphere/dome embryo run2", "D. rerio sphere/dome embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_sphere_dome_run2.fastq", "fastq", 82071009.0, 3039667.0, "CAGE   D. rerio sphere/dome embryo run2", "0:27", "A:20823133;C:17914934;G:22973465;T:20359477;N:0", 27, null, null, null, 20823133, 17914934, 22973465, 20359477, 0, "SRX156347", "SRS347208", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.47213, null, 0.07583, null, 0.82384, null, 0.8313, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36419, "SRR516551", "SRX156338", "SRS347207", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo oblong stage", "D. rerio oblong embryo", "D. rerio oblong embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio oblong embryo", "CAGE   D. rerio oblong embryo", "D. rerio oblong embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 135892080.0, 5033040.0, "CAGE   D. rerio oblong embryo", "0:27", "A:34565898;C:30442218;G:38967845;T:31916119;N:0", 27, null, null, null, 34565898, 30442218, 38967845, 31916119, 0, "SRX156338", "SRS347207", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.56265, null, 0.09335, null, 0.80068, null, 0.70759, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36420, "SRR516550", "SRX156337", "SRS347206", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo high stage", "D. rerio high embryo", "D. rerio high embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio high embryo", "CAGE   D. rerio high embryo", "D. rerio high embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_high.fastq", "fastq", 128592846.0, 4762698.0, "CAGE   D. rerio high embryo", "0:27", "A:33693838;C:27629256;G:36692263;T:30577489;N:0", 27, null, null, null, 33693838, 27629256, 36692263, 30577489, 0, "SRX156337", "SRS347206", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.53282, null, 0.08323, null, 0.80854, null, 0.77395, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2013-08-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36421, "SRR516549", "SRX156336", "SRS347204", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 512 cells stage", "D. rerio 512 cells embryo", "D. rerio 512 cells embyo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 512 cells embryo", "CAGE   D. rerio 512 cells embryo", "D. rerio 512 cells embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_512cells.fastq", "fastq", 150228810.0, 5564030.0, "CAGE   D. rerio 512 cells embryo", "0:27", "A:37826960;C:33838922;G:43403014;T:35159914;N:0", 27, null, null, null, 37826960, 33838922, 43403014, 35159914, 0, "SRX156336", "SRS347204", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.57925, null, 0.08753, null, 0.79933, null, 0.72579, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36422, "SRR516548", "SRX156334", "SRS347202", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo 64 cells stage", "D. rerio 64 cells embryo", "D. rerio 64 cells embryo", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio 64 cells embryo", "CAGE   D. rerio 64 cells embryo", "D. rerio 64 cells embryo", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_64cells.fastq", "fastq", 162784188.0, 6029044.0, "CAGE   D. rerio 64 cells embryo", "0:27", "A:41192860;C:36547869;G:46848833;T:38194626;N:0", 27, null, null, null, 41192860, 36547869, 46848833, 38194626, 0, "SRX156334", "SRS347202", "SRA055273", "University of Bergen", "ZEPROME consortium", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2013-08-31", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43058, "SRR8354695", "SRX5165478", "SRS4174524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 1", "DMS seq   RNA positives ctrl in vitro B1 AG01489", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1|barcode:TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 1", "AG01489.1", "AG01489.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01489.1_R1.fastq.gz", "fastq", 75703530.0, 2718404.0, "AG01489.1 R1.fastq.gz", "0:27.85 1:0", "A:18206335;C:19464567;G:21319876;T:16712584;N:168", 27, 0, null, null, 18206335, 19464567, 21319876, 16712584, 168, "SRX5165478", "SRS4174524", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.02389, null, 0.00591, null, 0.97654, null, 0.4758, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43059, "SRR8354696", "SRX5165477", "SRS4174523", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 2", "DMS seq   RNA positives ctrl in vitro B2 AG01490", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:2|barcode:GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS seq   RNA structure positive controls in vitro replicate 2", "AG01490.1", "AG01490.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01490.1_R1.fastq.gz", "fastq", 295051199.0, 10869746.0, "AG01490.1 R1.fastq.gz", "0:27.14 1:0", "A:71900468;C:76519029;G:81589099;T:65042019;N:584", 27, 0, null, null, 71900468, 76519029, 81589099, 65042019, 584, "SRX5165477", "SRS4174523", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.02362, null, 0.00528, null, 0.98173, null, 0.35096, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43060, "SRR8354697", "SRX5165476", "SRS4174522", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2", "Raw multiplex: DMS seq   RNA positives ctrl in vitro B1 AG01489;DMS seq   RNA positives ctrl in vitro B2 AG01490", null, "strain:TU/AB|age:3.7|dev stage:oblong|sex:pooled male and female|tissue:embryo|treatment:0.5% DMS for 10 min in vitro|molecule:RNA|condition:invitro DMS|replicate group:1|replicate:1;2|barcode:TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS seq   RNA structure positive controls in vitro replicate 1;DMS seq   RNA structure positive controls in vitro replicate 2", "AG01489.1;AG01490.1", "AG01489.1;AG01490.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBDX127_009_R1.fastq.gz", "fastq", 1115150128.0, 14673028.0, "C7MYYANXX JBDX127 009 R1.fastq.gz", "0:76", "A:313482382;C:276309346;G:291633361;T:233659719;N:65320", 76, null, null, null, 313482382, 276309346, 291633361, 233659719, 65320, "SRX5165476", "SRS4174522", "SRA825010", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00546, null, 0.00047, null, 0.98602, null, 0.51535, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-12-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43061, "SRR7264565", "SRX4168732", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.2;AG01047.2;AG01049.2;unrelated", "AG01046.2;AG01047.2;AG01049.2;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA22NADXX_JBBS71_021_R1.fastq.gz", "fastq", 493969676.0, 6499601.0, "HA22NADXX JBBS71 021 R1.fastq.gz", "0:76", "A:149523181;C:122615352;G:117180131;T:97949905;N:6701107", 76, null, null, null, 149523181, 122615352, 117180131, 97949905, 6701107, "SRX4168732", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43062, "SRR7264566", "SRX4168731", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "AG01046.1;AG01047.1;AG01049.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBS71_021_R1.fastq.gz", "fastq", 1444702012.0, 19009237.0, "HA1YWADXX JBBS71 021 R1.fastq.gz", "0:76", "A:442549747;C:365473385;G:344546726;T:292070542;N:61612", 76, null, null, null, 442549747, 365473385, 344546726, 292070542, 61612, "SRX4168731", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43063, "SRR7264567", "SRX4168730", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "AG01042.6;AG01043.6;AG01044.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBR70_020_R1.fastq.gz", "fastq", 3562176468.0, 46870743.0, "HBCAFADXX JBBR70 020 R1.fastq.gz", "0:76", "A:1097921080;C:906895047;G:849908073;T:707369464;N:82804", 76, null, null, null, 1097921080, 906895047, 849908073, 707369464, 82804, "SRX4168730", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43064, "SRR7264568", "SRX4168729", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "AG01042.5;AG01043.5;AG01044.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 13352386192.0, 175689292.0, "C562AACXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:4126007145;C:3372127203;G:3172182791;T:2661287884;N:20781169", 76, null, null, null, 4126007145, 3372127203, 3172182791, 2661287884, 20781169, "SRX4168729", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43065, "SRR7264569", "SRX4168728", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.4;AG01043.4;AG01044.4;unrelated", "AG01042.4;AG01043.4;AG01044.4;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA2H1ADXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 9139389880.0, 120255130.0, "HA2H1ADXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:2815354570;C:2322972018;G:2180978488;T:1817457488;N:2627316", 76, null, null, null, 2815354570, 2322972018, 2180978488, 1817457488, 2627316, "SRX4168728", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43066, "SRR7264570", "SRX4168727", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "AG01042.3;AG01043.3;AG01044.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBR70_NOBCX_R1.fastq.gz", "fastq", 7892000132.0, 103842107.0, "HA1YVADXX JBBR70 NOBCX R1.fastq.gz", "0:76", "A:2428266964;C:2007082407;G:1885147455;T:1568726692;N:2776614", 76, null, null, null, 2428266964, 2007082407, 1885147455, 1568726692, 2776614, "SRX4168727", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43067, "SRR7264571", "SRX4168726", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "AG01042.2;AG01043.2;AG01044.2;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA22NADXX_JBBR70_020_R1.fastq.gz", "fastq", 554569568.0, 7296968.0, "HA22NADXX JBBR70 020 R1.fastq.gz", "0:76", "A:168630291;C:138451887;G:131779810;T:108186590;N:7520990", 76, null, null, null, 168630291, 138451887, 131779810, 108186590, 7520990, "SRX4168726", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43068, "SRR7264572", "SRX4168725", "SRS3380690", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "Raw multiplex: dmsseq AG01042;dmsseq AG01043;dmsseq AG01044;unrelated", null, "strain:TU/AB|age:2.0;4.0;6.0|dev stage:64c;sphere;shield|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;15;16|replicate:1|barcode:CACA;AGAG;TCTC;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT sphere in vivo;DMS Seq   WT shield in vivo;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "AG01042.1;AG01043.1;AG01044.1;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YWADXX_JBBR70_020_R1.fastq.gz", "fastq", 1565371316.0, 20596991.0, "HA1YWADXX JBBR70 020 R1.fastq.gz", "0:76", "A:481887814;C:398331513;G:374271346;T:310815367;N:65276", 76, null, null, null, 481887814, 398331513, 374271346, 310815367, 65276, "SRX4168725", "SRS3380690", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43069, "SRR7264573", "SRX4168724", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "AG01046.4;AG01047.4;AG01049.4;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA2H1ADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 8845878184.0, 116393134.0, "HA2H1ADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2711637569;C:2235324807;G:2105535243;T:1791610098;N:1770467", 76, null, null, null, 2711637569, 2235324807, 2105535243, 1791610098, 1770467, "SRX4168724", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43070, "SRR7264574", "SRX4168723", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "AG01046.3;AG01047.3;AG01049.3;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HA1YVADXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 7768733452.0, 102220177.0, "HA1YVADXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:2378019627;C:1963788516;G:1851111018;T:1572409542;N:3404749", 76, null, null, null, 2378019627, 1963788516, 1851111018, 1572409542, 3404749, "SRX4168723", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43071, "SRR7264575", "SRX4168722", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.4;AG01274.4", "AG01273.4;AG01274.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HWKVWADXX_JBCZ103_023_R1.fastq.gz", "fastq", 7514617040.0, 98876540.0, "HWKVWADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367", 76, null, null, null, 2401597632, 1861527917, 1834777254, 1415956870, 757367, "SRX4168722", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43072, "SRR7264576", "SRX4168721", "SRS3380689", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2", "Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA   WT 64c RPF B1;RPF patA   WT 64c RPF B2", "AG01409.1;AG01410.1", "AG01409.1;AG01410.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDL115_014_R1.fastq.gz", "fastq", 4944760108.0, 65062633.0, "C7MPPANXX JBDL115 014 R1.fastq.gz", "0:76", "A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198", 76, null, null, null, 1280812305, 1385761238, 1441128504, 836702863, 355198, "SRX4168721", "SRS3380689", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43073, "SRR7264577", "SRX4168720", "SRS3380688", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2", "Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: RPF patA   WT 64c PatA RPF B1;RPF patA   WT 64c PatA RPF B2", "AG01411.1;AG01412.1", "AG01411.1;AG01412.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDM116_015_R1.fastq.gz", "fastq", 10995071544.0, 144671994.0, "C7MPPANXX JBDM116 015 R1.fastq.gz", "0:76", "A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089", 76, null, null, null, 2850888928, 3075001734, 3215965099, 1852417694, 798089, "SRX4168720", "SRS3380688", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43074, "SRR7264578", "SRX4168719", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.1;AG01427.1", "AG01426.1;AG01427.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDF109_027_R1.fastq.gz", "fastq", 446991948.0, 5881473.0, "C7MPPANXX JBDF109 027 R1.fastq.gz", "0:76", "A:146192524;C:109441919;G:103882304;T:87445288;N:29913", 76, null, null, null, 146192524, 109441919, 103882304, 87445288, 29913, "SRX4168719", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43075, "SRR7264579", "SRX4168718", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.2;AG01427.2", "AG01426.2;AG01427.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDF109_027_R1.fastq.gz", "fastq", 447485492.0, 5887967.0, "HVJC2ADXX JBDF109 027 R1.fastq.gz", "0:76", "A:146683880;C:109166579;G:104154702;T:87473352;N:6979", 76, null, null, null, 146683880, 109166579, 104154702, 87473352, 6979, "SRX4168718", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0023, null, 0.00034, null, 0.99326, null, 0.57567, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43076, "SRR7264580", "SRX4168717", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.3;AG01427.3", "AG01426.3;AG01427.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDF109_027_R1.fastq.gz", "fastq", 4740289176.0, 62372226.0, "HVJ2TADXX JBDF109 027 R1.fastq.gz", "0:76", "A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336", 76, null, null, null, 1552060471, 1156267615, 1104246757, 927209997, 504336, "SRX4168717", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00235, null, 0.00026, null, 0.99379, null, 0.60051, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43077, "SRR7264581", "SRX4168716", "SRS3380687", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c DMS B1;DMS Seq PatA   WT 64c DMS B2", "AG01426.4;AG01427.4", "AG01426.4;AG01427.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz", "fastq", 6776423036.0, 89163461.0, "HJTYNBCXX JBDF109 NOBCX R1.fastq.gz", "0:76", "A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906", 76, null, null, null, 2212424663, 1653496002, 1573846163, 1336100302, 555906, "SRX4168716", "SRS3380687", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43078, "SRR7264582", "SRX4168715", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.1;AG01429.1", "AG01428.1;AG01429.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MPPANXX_JBDG110_013_R1.fastq.gz", "fastq", 1593732388.0, 20970163.0, "C7MPPANXX JBDG110 013 R1.fastq.gz", "0:76", "A:517196379;C:393268952;G:372639155;T:310521534;N:106368", 76, null, null, null, 517196379, 393268952, 372639155, 310521534, 106368, "SRX4168715", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43079, "SRR7264583", "SRX4168714", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.2;AG01429.2", "AG01428.2;AG01429.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJC2ADXX_JBDG110_013_R1.fastq.gz", "fastq", 1268326988.0, 16688513.0, "HVJC2ADXX JBDG110 013 R1.fastq.gz", "0:76", "A:411772190;C:312434121;G:297408612;T:246654231;N:57834", 76, null, null, null, 411772190, 312434121, 297408612, 246654231, 57834, "SRX4168714", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43080, "SRR7264584", "SRX4168713", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.3;AG01429.3", "AG01428.3;AG01429.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ2TADXX_JBDG110_013_R1.fastq.gz", "fastq", 1149592188.0, 15126213.0, "HVJ2TADXX JBDG110 013 R1.fastq.gz", "0:76", "A:373090462;C:283151050;G:269811169;T:223419849;N:119658", 76, null, null, null, 373090462, 283151050, 269811169, 223419849, 119658, "SRX4168713", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00222, null, 0.0002, null, 0.99362, null, 0.55643, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43081, "SRR7264585", "SRX4168712", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.3;AG01274.3", "AG01273.3;AG01274.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCZ103_023_R1.fastq.gz", "fastq", 882016024.0, 11605474.0, "HVJ7NADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:278837606;C:213606139;G:214029888;T:175477675;N:64716", 76, null, null, null, 278837606, 213606139, 214029888, 175477675, 64716, "SRX4168712", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 6e-05, null, 4e-05, null, 0.99995, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43082, "SRR7264586", "SRX4168711", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.2;AG01274.2", "AG01273.2;AG01274.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2614864056.0, 34406106.0, "HVK53ADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:832670351;C:647746556;G:639758530;T:494461931;N:226688", 76, null, null, null, 832670351, 647746556, 639758530, 494461931, 226688, "SRX4168711", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 5e-05, null, 2e-05, null, 0.99993, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43083, "SRR7264587", "SRX4168710", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.4;AG01270.4", "AG01269.4;AG01270.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBCX101_016_R1.fastq.gz", "fastq", 3504515800.0, 46112050.0, "C7MYYANXX JBCX101 016 R1.fastq.gz", "0:76", "A:1100987855;C:897481291;G:850509260;T:655386223;N:151171", 76, null, null, null, 1100987855, 897481291, 850509260, 655386223, 151171, "SRX4168710", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00251, null, 0.00024, null, 0.99334, null, 0.49363, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43084, "SRR7264588", "SRX4168709", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.3;AG01270.3", "AG01269.3;AG01270.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCX101_016_R1.fastq.gz", "fastq", 1533760484.0, 20181059.0, "HVJ7NADXX JBCX101 016 R1.fastq.gz", "0:76", "A:486730101;C:387546602;G:372319444;T:287072948;N:91389", 76, null, null, null, 486730101, 387546602, 372319444, 287072948, 91389, "SRX4168709", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 4e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43085, "SRR7264589", "SRX4168708", "SRS3380686", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "Raw multiplex: dmsseq AG01273;dmsseq AG01274", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c CHX B1;DMS Seq   WT 64c CHX B2", "AG01273.1;AG01274.1", "AG01273.1;AG01274.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCZ103_023_R1.fastq.gz", "fastq", 2819768568.0, 37102218.0, "HMHGVADXX JBCZ103 023 R1.fastq.gz", "0:76", "A:900945260;C:699348182;G:689446355;T:529699985;N:328786", 76, null, null, null, 900945260, 699348182, 689446355, 529699985, 328786, "SRX4168708", "SRS3380686", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43086, "SRR7264590", "SRX4168707", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.5;AG01270.5", "AG01269.5;AG01270.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MWLANXX_JBCX101_016_R1.fastq.gz", "fastq", 11187105076.0, 147198751.0, "C7MWLANXX JBCX101 016 R1.fastq.gz", "0:76", "A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660", 76, null, null, null, 3525623658, 2869684594, 2708534500, 2083102664, 159660, "SRX4168707", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43087, "SRR7264591", "SRX4168706", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "AG01046.6;AG01047.6;AG01049.6;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "HBCAFADXX_JBBS71_021_R1.fastq.gz", "fastq", 5103002976.0, 67144776.0, "HBCAFADXX JBBS71 021 R1.fastq.gz", "0:76", "A:1565087315;C:1292145008;G:1214936605;T:1030712352;N:121696", 76, null, null, null, 1565087315, 1292145008, 1214936605, 1030712352, 121696, "SRX4168706", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43088, "SRR7264592", "SRX4168705", "SRS3380685", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "Raw multiplex: dmsseq AG01046;dmsseq AG01047;dmsseq AG01049;unrelated", null, "strain:TU/AB|age:2.0;6.0;4.0|dev stage:64c;shield;sphere|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14;16;15|replicate:2|barcode:CACA;TCTC;AGAG;GTGT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   WT 64c in vivo;DMS Seq   WT shield in vivo;DMS Seq   WT sphere in vivo;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "AG01046.5;AG01047.5;AG01049.5;unrelated", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP114782", null, null, "C562AACXX_JBBS71_NOBCX_R1.fastq.gz", "fastq", 11245730944.0, 147970144.0, "C562AACXX JBBS71 NOBCX R1.fastq.gz", "0:76", "A:3451642355;C:2826476753;G:2670179644;T:2277897894;N:19534298", 76, null, null, null, 3451642355, 2826476753, 2670179644, 2277897894, 19534298, "SRX4168705", "SRS3380685", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43089, "SRR7264593", "SRX4168704", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.2;AG01270.2", "AG01269.2;AG01270.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCX101_016_R1.fastq.gz", "fastq", 4318423208.0, 56821358.0, "HVK53ADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019", 76, null, null, null, 1370691469, 1101595011, 1048719303, 796936406, 481019, "SRX4168704", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43090, "SRR7264594", "SRX4168703", "SRS3380684", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.1;AG01270.1", "AG01269.1;AG01270.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCX101_016_R1.fastq.gz", "fastq", 3247405520.0, 42729020.0, "HMHGVADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1030573532;C:829398246;G:789085434;T:598013908;N:334400", 76, null, null, null, 1030573532, 829398246, 789085434, 598013908, 334400, "SRX4168703", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43091, "SRR7264595", "SRX4168702", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.5;AG01429.5", "AG01428.5;AG01429.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HJTYNBCXX_JBDG110_NOBCX_R1.fastq.gz", "fastq", 8473348224.0, 111491424.0, "HJTYNBCXX JBDG110 NOBCX R1.fastq.gz", "0:76", "A:2738474380;C:2086110939;G:1986494866;T:1661471870;N:796169", 76, null, null, null, 2738474380, 2086110939, 1986494866, 1661471870, 796169, "SRX4168702", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 3e-05, null, 2e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43092, "SRR7264596", "SRX4168701", "SRS3380683", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq PatA   WT 64c PatA DMS B1;DMS Seq PatA   WT 64c PatA DMS B2", "AG01428.4;AG01429.4", "AG01428.4;AG01429.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBDG110_013_R1.fastq.gz", "fastq", 1317100672.0, 17330272.0, "HVJ7NADXX JBDG110 013 R1.fastq.gz", "0:76", "A:424319849;C:318879376;G:308835829;T:264971153;N:94465", 76, null, null, null, 424319849, 318879376, 308835829, 264971153, 94465, "SRX4168701", "SRS3380683", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 9e-05, null, 5e-05, null, 0.99995, null, 0.2, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43093, "SRR5893052", "SRX3058793", "SRS2404523", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h a Am pA RNA B1", "miniresa AG01714", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h a Am pA RNA B1", "AG01714.1", "AG01714.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01714.1_R1.fastq.gz", "fastq", 263900576.0, 3472376.0, "AG01714.1 R1.fastq.gz", "0:76", "A:71973779;C:48927629;G:51913512;T:91079622;N:6034", 76, null, null, null, 71973779, 48927629, 51913512, 91079622, 6034, "SRX3058793", "SRS2404523", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9163, null, 3e-05, null, 0.99833, null, 0.61085, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43094, "SRR5893053", "SRX3058792", "SRS2404525", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   6h a Am pA RNA B2", "miniresa AG01715", null, "strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|replicate group:27|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   6h a Am pA RNA B2", "AG01715.1", "AG01715.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01715.1_R1.fastq.gz", "fastq", 233910976.0, 3077776.0, "AG01715.1 R1.fastq.gz", "0:76", "A:63827548;C:43163354;G:46127646;T:80731865;N:60563", 76, null, null, null, 63827548, 43163354, 46127646, 80731865, 60563, "SRX3058792", "SRS2404525", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92571, null, 3e-05, null, 0.99809, null, 0.62106, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43095, "SRR5893054", "SRX3058791", "SRS2404524", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   2h pA RNA B1", "miniresa AG01710", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B1", "AG01710.1", "AG01710.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01710.1_R1.fastq.gz", "fastq", 236178588.0, 3107613.0, "AG01710.1 R1.fastq.gz", "0:76", "A:63902747;C:43772893;G:46507615;T:81990822;N:4511", 76, null, null, null, 63902747, 43772893, 46507615, 81990822, 4511, "SRX3058791", "SRS2404524", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92111, null, 4e-05, null, 0.99799, null, 0.56316, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43096, "SRR5893055", "SRX3058790", "SRS2404526", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.", null, null, null, "miniRESA   2h pA RNA B2", "miniresa AG01711", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B2", "AG01711.1", "AG01711.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01711.1_R1.fastq.gz", "fastq", 226089360.0, 2974860.0, "AG01711.1 R1.fastq.gz", "0:76", "A:61341697;C:41846683;G:44622362;T:78273216;N:5402", 76, null, null, null, 61341697, 41846683, 44622362, 78273216, 5402, "SRX3058790", "SRS2404526", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91845, null, 1e-05, null, 0.99797, null, 0.60522, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43097, "SRR5893056", "SRX3058789", "SRS2404529", "SRP114782", "PRJNA397065", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis", "PRJNA397065", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. 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However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. 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However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. 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However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. 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However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. 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