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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 97 individuals", "Dr bud 2", "SAMD00028154", null, "sample name:Dr bud 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028154", "DRX029563", "Dr bud 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028154", null, null, null, 4104778200.0, 41047782.0, "DRR032757", "0:100 1:0", "A:1116316188;C:944738800;G:936257056;T:1107423486;N:42670", 100, 0, null, null, 1116316188, 944738800, 936257056, 1107423486, 42670, "DRX029563", "DRS049962", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92945, null, 0.10493, null, 0.73407, null, 0.47824, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [68, "DRR032756", "DRX029562", "DRS049961", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 90epiboly 2", "SAMD00028152", null, "sample name:Dr 90epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028152", "DRX029561", "Dr 90epiboly 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028152", null, null, null, 3572358600.0, 35723586.0, "DRR032755", "0:100 1:0", "A:971653450;C:821326559;G:816855636;T:962477457;N:45498", 100, 0, null, null, 971653450, 821326559, 816855636, 962477457, 45498, "DRX029561", "DRS049960", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92485, null, 0.10642, null, 0.74213, null, 0.47012, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [70, "DRR032754", "DRX029560", "DRS049959", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 90epiboly 1", "SAMD00028151", null, "sample name:Dr 90epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028151", "DRX029560", "Dr 90epiboly 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028151", null, null, null, 3423980500.0, 34239805.0, "DRR032754", "0:100 1:0", "A:933088185;C:785251613;G:780911148;T:924686406;N:43148", 100, 0, null, null, 933088185, 785251613, 780911148, 924686406, 43148, "DRX029560", "DRS049959", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92436, null, 0.10881, null, 0.74255, null, 0.47068, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [71, "DRR032753", "DRX029559", "DRS049958", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 114 individuals", "Dr 8cell 2", "SAMD00028150", null, "sample name:Dr 8cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028150", "DRX029559", "Dr 8cell 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028150", null, null, null, 3708921900.0, 37089219.0, "DRR032753", "0:100 1:0", "A:985502141;C:874161613;G:869551685;T:979663686;N:42775", 100, 0, null, null, 985502141, 874161613, 869551685, 979663686, 42775, "DRX029559", "DRS049958", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.93329, null, 0.02366, null, 0.78896, null, 0.47447, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [72, "DRR032752", "DRX029558", "DRS049957", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 96 individuals", "Dr 8cell 1", "SAMD00028149", null, "sample name:Dr 8cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028149", "DRX029558", "Dr 8cell 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028149", null, null, null, 3666991200.0, 36669912.0, "DRR032752", "0:100 1:0", "A:976118513;C:862559696;G:858017821;T:970254302;N:40868", 100, 0, null, null, 976118513, 862559696, 858017821, 970254302, 40868, "DRX029558", "DRS049957", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.934, null, 0.02403, null, 0.78877, null, 0.46902, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [73, "DRR032751", "DRX029557", "DRS049956", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 75epiboly 2", "SAMD00028148", null, "sample name:Dr 75epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028148", "DRX029557", "Dr 75epiboly 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028148", null, null, null, 3252021500.0, 32520215.0, "DRR032751", "0:100 1:0", "A:885527595;C:746750899;G:742907892;T:876794123;N:40991", 100, 0, null, null, 885527595, 746750899, 742907892, 876794123, 40991, "DRX029557", "DRS049956", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92594, null, 0.10181, null, 0.74862, null, 0.47789, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [74, "DRR032750", "DRX029556", "DRS049955", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 75epiboly 1", "SAMD00028147", null, "sample name:Dr 75epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028147", "DRX029556", "Dr 75epiboly 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028147", null, null, null, 3785053700.0, 37850537.0, "DRR032750", "0:100 1:0", "A:1029014798;C:870946157;G:867537069;T:1017508684;N:46992", 100, 0, null, null, 1029014798, 870946157, 867537069, 1017508684, 46992, "DRX029556", "DRS049955", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92346, null, 0.10046, null, 0.74921, null, 0.47295, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [75, "DRR032749", "DRX029555", "DRS049954", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 72h 2", "SAMD00028146", null, "sample name:Dr 72h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028146", "DRX029555", "Dr 72h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028146", null, null, null, 3429795800.0, 34297958.0, "DRR032749", "0:100 1:0", "A:928062015;C:792470305;G:786930881;T:922296289;N:36310", 100, 0, null, null, 928062015, 792470305, 786930881, 922296289, 36310, "DRX029555", "DRS049954", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.91821, null, 0.09774, null, 0.65437, null, 0.46443, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [76, "DRR032748", "DRX029554", "DRS049953", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 72h 1", "SAMD00028145", null, "sample name:Dr 72h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028145", "DRX029554", "Dr 72h 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028145", null, null, null, 3897194500.0, 38971945.0, "DRR032748", "0:100 1:0", "A:1050989414;C:903225496;G:895783177;T:1047153493;N:42920", 100, 0, null, null, 1050989414, 903225496, 895783177, 1047153493, 42920, "DRX029554", "DRS049953", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92211, null, 0.09393, null, 0.65486, null, 0.45971, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [77, "DRR032747", "DRX029553", "DRS049952", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 6somite 2", "SAMD00028144", null, "sample name:Dr 6somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028144", "DRX029553", "Dr 6somite 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028144", null, null, null, 3704431000.0, 37044310.0, "DRR032747", "0:100 1:0", "A:1001844161;C:856702913;G:850695568;T:995148798;N:39560", 100, 0, null, null, 1001844161, 856702913, 850695568, 995148798, 39560, "DRX029553", "DRS049952", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92633, null, 0.09211, null, 0.72107, null, 0.47195, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [78, "DRR032746", "DRX029552", "DRS049951", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 6somite 1", "SAMD00028143", null, "sample name:Dr 6somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028143", "DRX029552", "Dr 6somite 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028143", null, null, null, 3529311900.0, 35293119.0, "DRR032746", "0:100 1:0", "A:953957996;C:816824469;G:811403696;T:947089530;N:36209", 100, 0, null, null, 953957996, 816824469, 811403696, 947089530, 36209, "DRX029552", "DRS049951", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92437, null, 0.09257, null, 0.72113, null, 0.47004, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [79, "DRR032745", "DRX029551", "DRS049950", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 60h 2", "SAMD00028142", null, "sample name:Dr 60h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028142", "DRX029551", "Dr 60h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028142", null, null, null, 3875337000.0, 38753370.0, "DRR032745", "0:100 1:0", "A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983", 100, 0, null, null, 1042558903, 899892111, 896867583, 1035981420, 36983, "DRX029551", "DRS049950", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.91891, null, 0.09445, null, 0.66156, null, 0.45564, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [80, "DRR032744", "DRX029550", "DRS049949", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 5day 3", "SAMD00028140", null, "sample name:Dr 5day 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028140", "DRX029549", "Dr 5day 3", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028140", null, null, null, 3884716000.0, 38847160.0, "DRR032743", "0:100 1:0", "A:1040550584;C:905663425;G:904247323;T:1034215019;N:39649", 100, 0, null, null, 1040550584, 905663425, 904247323, 1034215019, 39649, "DRX029549", "DRS049948", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92219, null, 0.08287, null, 0.65863, null, 0.47377, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [82, "DRR032742", "DRX029548", "DRS049947", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 48h 2", "SAMD00028137", null, "sample name:Dr 48h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028137", "DRX029546", "Dr 48h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028137", null, null, null, 3702804700.0, 37028047.0, "DRR032740", "0:100 1:0", "A:993931475;C:862403562;G:857808891;T:988623734;N:37038", 100, 0, null, null, 993931475, 862403562, 857808891, 988623734, 37038, "DRX029546", "DRS049945", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92508, null, 0.08526, null, 0.68349, null, 0.45769, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [85, "DRR032739", "DRX029545", "DRS049944", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 32cell 2", "SAMD00028135", null, "sample name:Dr 32cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028135", "DRX029544", "Dr 32cell 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028135", null, null, null, 3678713000.0, 36787130.0, "DRR032738", "0:100 1:0", "A:981005900;C:863203049;G:859660640;T:974807835;N:35576", 100, 0, null, null, 981005900, 863203049, 859660640, 974807835, 35576, "DRX029544", "DRS049943", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.93302, null, 0.02468, null, 0.77441, null, 0.47485, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [87, "DRR032737", "DRX029543", "DRS049942", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 80 individuals", "Dr 14somite 3", "SAMD00028129", null, "sample name:Dr 14somite 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028129", "DRX029538", "Dr 14somite 3", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028129", null, null, null, 3734610500.0, 37346105.0, "DRR032732", "0:100 1:0", "A:1009418541;C:863710067;G:858061383;T:1003378800;N:41709", 100, 0, null, null, 1009418541, 863710067, 858061383, 1003378800, 41709, "DRX029538", "DRS049937", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92401, null, 0.08815, null, 0.70816, null, 0.46602, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [93, "DRR032731", "DRX029537", "DRS049936", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.", null, null, "mRNA extracted from pooled embryos of 80 individuals", "Dr 14somite 2", "SAMD00028128", null, "sample name:Dr 14somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male  female  and mixed", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028128", "DRX029537", "Dr 14somite 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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>", "DRP003810", "Illumina HiSeq 2000 sequencing of SAMD00028128", null, null, null, 3715174200.0, 37151742.0, "DRR032731", "0:100 1:0", "A:1000703508;C:862290629;G:858173468;T:993968396;N:38199", 100, 0, null, null, 1000703508, 862290629, 858173468, 993968396, 38199, "DRX029537", "DRS049936", "DRA003460", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", "UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo", 1, 0.92491, null, 0.0819, null, 0.71068, null, 0.46957, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [94, "DRR032730", "DRX029536", "DRS049935", "DRP003810", "PRJDB3785", "EXPANDE project", "DRP003810", "Other", "EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. 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We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. 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Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 4Ei", "SAMEA6504165", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 1", "Shield 4Ei SSU", "OTHER", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 7154041880.0, 94132130.0, "ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 1", "0:76", "A:2939474250;C:1489083073;G:1922522149;T:802890185;N:72223", 76, null, null, null, 2939474250, 1489083073, 1922522149, 802890185, 72223, "ERX3854563", "ERS4268611", "ERA2359340", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.4369, null, 0.25417, null, 0.9867, null, 0.60047, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9719, "ERR3842000", "ERX3854562", "ERS4268611", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. 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We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. 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We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. 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Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 4150NT", "SAMEA5752548", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 8", "Shield 150NT", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1188343980.0, 15636105.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 8", "0:76", "A:580658556;C:223116826;G:260847322;T:123709681;N:11595", 76, null, null, null, 580658556, 223116826, 260847322, 123709681, 11595, "ERX3854560", "ERS3556007", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.27037, null, 0.13972, null, 0.97392, null, 0.39459, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9722, "ERR3841997", "ERX3854559", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 7", "Shield 1", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1278891444.0, 16827519.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 7", "0:76", "A:571738369;C:256385478;G:295145281;T:155610082;N:12234", 76, null, null, null, 571738369, 256385478, 295145281, 155610082, 12234, "ERX3854559", "ERS3556004", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.23116, null, 0.11137, null, 0.97932, null, 0.45978, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9723, "ERR3841996", "ERX3854558", "ERS3556001", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 3", "SAMEA5752542", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 6", "Sphere 3", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1439954368.0, 18946768.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 6", "0:76", "A:669362698;C:280496524;G:316727778;T:173353505;N:13863", 76, null, null, null, 669362698, 280496524, 316727778, 173353505, 13863, "ERX3854558", "ERS3556001", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.26155, null, 0.12068, null, 0.96915, null, 0.45719, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9724, "ERR3841995", "ERX3854557", "ERS3556000", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 2", "SAMEA5752541", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 5", "Sphere 2", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1592272200.0, 20950950.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 5", "0:76", "A:757507948;C:308394094;G:342142775;T:184211881;N:15502", 76, null, null, null, 757507948, 308394094, 342142775, 184211881, 15502, "ERX3854557", "ERS3556000", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.22483, null, 0.10923, null, 0.97646, null, 0.49458, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9725, "ERR3841994", "ERX3854556", "ERS3555999", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 1", "SAMEA5752540", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 4", "Sphere 1", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1332363676.0, 17531101.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 4", "0:76", "A:529354355;C:299445923;G:318745973;T:184804260;N:13165", 76, null, null, null, 529354355, 299445923, 318745973, 184804260, 13165, "ERX3854556", "ERS3555999", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.21197, null, 0.0829, null, 0.98196, null, 0.55753, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9726, "ERR3841993", "ERX3854555", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 3", "64 cell 3", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1579307816.0, 20780366.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 3", "0:76", "A:589876602;C:380048242;G:392473318;T:216893826;N:15828", 76, null, null, null, 589876602, 380048242, 392473318, 216893826, 15828, "ERX3854555", "ERS3555998", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.15411, null, 0.04564, null, 0.97883, null, 0.55376, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9727, "ERR3841992", "ERX3854554", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 2", "64 cell 4Ei", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1213585480.0, 15968230.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 2", "0:76", "A:548456563;C:244465528;G:271963808;T:148687764;N:11817", 76, null, null, null, 548456563, 244465528, 271963808, 148687764, 11817, "ERX3854554", "ERS3556003", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.21973, null, 0.10926, null, 0.97419, null, 0.44348, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9728, "ERR3841991", "ERX3854553", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:405 1", "64 cell 1", "OTHER", "RNA Seq", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14", null, null, 1494930944.0, 19670144.0, "ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 1", "0:76", "A:543017836;C:366974203;G:367027373;T:217896401;N:15131", 76, null, null, null, 543017836, 366974203, 367027373, 217896401, 15131, "ERX3854553", "ERS3555997", "ERA2359305", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.2544, null, 0.08957, null, 0.96568, null, 0.55681, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9729, "ERR3489881", "ERX3511296", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 33", "Shield 1 F20", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 975578636.0, 12836561.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 33", "0:76", "A:398325549;C:237563934;G:230721299;T:108957698;N:10156", 76, null, null, null, 398325549, 237563934, 230721299, 108957698, 10156, "ERX3511296", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.33102, null, 0.19766, null, 0.99918, null, 0.12812, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9730, "ERR3489880", "ERX3511295", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 32", "Shield 1 F19", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 931166668.0, 12252193.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 32", "0:76", "A:271081669;C:253947035;G:272354427;T:133774815;N:8722", 76, null, null, null, 271081669, 253947035, 272354427, 133774815, 8722, "ERX3511295", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.15598, null, 0.10707, null, 0.99902, null, 0.47314, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9731, "ERR3489879", "ERX3511294", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 31", "Shield 1 F18", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1506513268.0, 19822543.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 31", "0:76", "A:493273515;C:456544968;G:391677033;T:165002559;N:15193", 76, null, null, null, 493273515, 456544968, 391677033, 165002559, 15193, "ERX3511294", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.01562, null, 0.0053, null, 0.99908, null, 0.8127, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9732, "ERR3489878", "ERX3511293", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 30", "Shield 1 F17", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1259456496.0, 16571796.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 30", "0:76", "A:471473123;C:333726472;G:302016190;T:152228002;N:12709", 76, null, null, null, 471473123, 333726472, 302016190, 152228002, 12709, "ERX3511293", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.18339, null, 0.12544, null, 0.99928, null, 0.22368, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9733, "ERR3489877", "ERX3511292", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 29", "Shield 1 F16", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1364615872.0, 17955472.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 29", "0:76", "A:539462776;C:341141880;G:314571683;T:169426048;N:13485", 76, null, null, null, 539462776, 341141880, 314571683, 169426048, 13485, "ERX3511292", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.11663, null, 0.07319, null, 0.99939, null, 0.25377, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9734, "ERR3489876", "ERX3511291", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 28", "Shield 1 F15", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 952605888.0, 12534288.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 28", "0:76", "A:414133320;C:219437277;G:207418049;T:111607418;N:9824", 76, null, null, null, 414133320, 219437277, 207418049, 111607418, 9824, "ERX3511291", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.17603, null, 0.10972, null, 0.99935, null, 0.13311, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9735, "ERR3489875", "ERX3511290", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 27", "Shield 1 F14", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 870952628.0, 11459903.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 27", "0:76", "A:357710338;C:221475453;G:191231014;T:100526675;N:9148", 76, null, null, null, 357710338, 221475453, 191231014, 100526675, 9148, "ERX3511290", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.1248, null, 0.06422, null, 0.99896, null, 0.34819, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9736, "ERR3489874", "ERX3511289", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 26", "Shield 1 F13", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 981672620.0, 12916745.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 26", "0:76", "A:434153198;C:223317075;G:198260771;T:125932145;N:9431", 76, null, null, null, 434153198, 223317075, 198260771, 125932145, 9431, "ERX3511289", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.44603, null, 0.25602, null, 0.99874, null, 0.18074, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9737, "ERR3489873", "ERX3511288", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 25", "Shield 1 F12", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1304618128.0, 17166028.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 25", "0:76", "A:651341516;C:270458496;G:243929520;T:138874830;N:13766", 76, null, null, null, 651341516, 270458496, 243929520, 138874830, 13766, "ERX3511288", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.64293, null, 0.38159, null, 0.99886, null, 0.07313, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9738, "ERR3489872", "ERX3511287", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 24", "Shield 1 F10", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1336115948.0, 17580473.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 24", "0:76", "A:608634206;C:295943144;G:286494431;T:145029697;N:14470", 76, null, null, null, 608634206, 295943144, 286494431, 145029697, 14470, "ERX3511287", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.68758, null, 0.47517, null, 0.99898, null, 0.02301, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9739, "ERR3489871", "ERX3511286", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 23", "Shield 1 F9", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 1434402492.0, 18873717.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 23", "0:76", "A:658705664;C:297967081;G:295595736;T:182118632;N:15379", 76, null, null, null, 658705664, 297967081, 295595736, 182118632, 15379, "ERX3511286", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.74246, null, 0.44235, null, 0.99701, null, 0.03112, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9740, "ERR3489870", "ERX3511285", "ERS3556007", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 4150NT", "SAMEA5752548", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 22", "Shield 4150NT LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24", null, null, 24063208094.0, 159358994.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 22", "0:151", "A:7153064588;C:5242791119;G:8513736630;T:3152547276;N:1068481", 151, null, null, null, 7153064588, 5242791119, 8513736630, 3152547276, 1068481, "ERX3511285", "ERS3556007", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.81267, null, 0.27138, null, 0.99868, null, 0.91938, null, 151, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9741, "ERR3489869", "ERX3511284", "ERS3556007", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 4150NT", "SAMEA5752548", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 21", "Shield 4150NT SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24", null, null, 14987998619.0, 99258269.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 21", "0:151", "A:4578051806;C:2616328922;G:5914185813;T:1878780090;N:651988", 151, null, null, null, 4578051806, 2616328922, 5914185813, 1878780090, 651988, "ERX3511284", "ERS3556007", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.77096, null, 0.5278, null, 0.99833, null, 0.42635, null, 151, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9742, "ERR3489868", "ERX3511283", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 20", "64 cell 4Ei 10 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 5928054796.0, 78000721.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 20", "0:76", "A:2109854905;C:1377083508;G:1616166285;T:824889630;N:60468", 76, null, null, null, 2109854905, 1377083508, 1616166285, 824889630, 60468, "ERX3511283", "ERS3556003", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.61525, null, 0.45233, null, 0.99379, null, 0.57373, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9743, "ERR3489867", "ERX3511282", "ERS3556003", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 10", "SAMEA5752544", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 19", "64 cell 4Ei 10 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9772604780.0, 128586905.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 19", "0:76", "A:3901301079;C:2223067879;G:2553338016;T:1094797648;N:100158", 76, null, null, null, 3901301079, 2223067879, 2553338016, 1094797648, 100158, "ERX3511282", "ERS3556003", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.52103, null, 0.25046, null, 0.9861, null, 0.64575, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9744, "ERR3489866", "ERX3511281", "ERS3556002", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 0.1", "SAMEA5752543", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 18", "64 cell 4Ei 0.1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26", null, null, 6730725680.0, 88562180.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 18", "0:76", "A:3805722011;C:1188715051;G:1382258076;T:353814168;N:216374", 76, null, null, null, 3805722011, 1188715051, 1382258076, 353814168, 216374, "ERX3511281", "ERS3556002", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.61922, null, 0.37217, null, 0.99527, null, 0.29148, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9745, "ERR3489865", "ERX3511280", "ERS3556002", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 4Ei 0.1", "SAMEA5752543", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 17", "64 cell 4Ei 0.1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26", null, null, 10616304872.0, 139688222.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 17", "0:76", "A:4717003484;C:2600725234;G:2586105174;T:712124440;N:346540", 76, null, null, null, 4717003484, 2600725234, 2586105174, 712124440, 346540, "ERX3511280", "ERS3556002", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.30908, null, 0.08252, null, 0.94683, null, 0.69548, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9746, "ERR3489864", "ERX3511279", "ERS3556006", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 3", "SAMEA5752547", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752547|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:10|common name:zebrafish|dev stage:Shield|sample name:10|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 16", "Shield 3 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 11777220072.0, 154963422.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 16", "0:76", "A:3368038444;C:3190496935;G:3529701152;T:1688766119;N:217422", 76, null, null, null, 3368038444, 3190496935, 3529701152, 1688766119, 217422, "ERX3511279", "ERS3556006", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.70681, null, 0.18846, null, 0.99332, null, 0.71978, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9747, "ERR3489863", "ERX3511278", "ERS3556006", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 3", "SAMEA5752547", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752547|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:10|common name:zebrafish|dev stage:Shield|sample name:10|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 15", "Shield 3 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 7920419952.0, 104216052.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 15", "0:76", "A:2990167185;C:1767708808;G:2104830363;T:1057568560;N:145036", 76, null, null, null, 2990167185, 1767708808, 2104830363, 1057568560, 145036, "ERX3511278", "ERS3556006", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.5052, null, 0.30841, null, 0.99129, null, 0.60948, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9748, "ERR3489862", "ERX3511277", "ERS3556005", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 2", "SAMEA5752546", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752546|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:9|common name:zebrafish|dev stage:Shield|sample name:9|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 14", "Shield 2 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9775297004.0, 128622329.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 14", "0:76", "A:4750565405;C:2540992255;G:1698817649;T:784832634;N:89061", 76, null, null, null, 4750565405, 2540992255, 1698817649, 784832634, 89061, "ERX3511277", "ERS3556005", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.74003, null, 0.5616, null, 0.99855, null, 0.03607, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9749, "ERR3489861", "ERX3511276", "ERS3556005", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 2", "SAMEA5752546", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752546|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:9|common name:zebrafish|dev stage:Shield|sample name:9|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 13", "Shield 2 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 8210103300.0, 108027675.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 13", "0:76", "A:3300825043;C:2576709678;G:1707115198;T:625376255;N:77126", 76, null, null, null, 3300825043, 2576709678, 1707115198, 625376255, 77126, "ERX3511276", "ERS3556005", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.2787, null, 0.17583, null, 0.99752, null, 0.50171, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9750, "ERR3489860", "ERX3511275", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 12", "Shield 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 2437679936.0, 32074736.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 12", "0:76", "A:764355184;C:710492003;G:664031460;T:298777374;N:23915", 76, null, null, null, 764355184, 710492003, 664031460, 298777374, 23915, "ERX3511275", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.0406, null, 0.02417, null, 0.99908, null, 0.61299, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9751, "ERR3489859", "ERX3511274", "ERS3556004", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Shield 1", "SAMEA5752545", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 11", "Shield 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 3157243376.0, 41542676.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 11", "0:76", "A:1443205052;C:715251024;G:633421305;T:365333650;N:32345", 76, null, null, null, 1443205052, 715251024, 633421305, 365333650, 32345, "ERX3511274", "ERS3556004", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.47643, null, 0.27944, null, 0.99896, null, 0.11464, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Gastrula", "Embryo", "Undetermined", "Embryo Imprecise"], [9752, "ERR3489858", "ERX3511273", "ERS3556001", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 3", "SAMEA5752542", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 10", "Sphere 3 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 2740392724.0, 36057799.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 10", "0:76", "A:1790452280;C:354001675;G:431182140;T:164697730;N:58899", 76, null, null, null, 1790452280, 354001675, 431182140, 164697730, 58899, "ERX3511273", "ERS3556001", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.87154, null, 0.5323, null, 0.99793, null, 0.02983, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9753, "ERR3489857", "ERX3511272", "ERS3556001", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 3", "SAMEA5752542", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 9", "Sphere 3 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 6277242192.0, 82595292.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 9", "0:76", "A:3129446012;C:1311888416;G:1369035262;T:466745503;N:126999", 76, null, null, null, 3129446012, 1311888416, 1369035262, 466745503, 126999, "ERX3511272", "ERS3556001", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.65637, null, 0.35975, null, 0.9936, null, 0.24734, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9754, "ERR3489856", "ERX3511271", "ERS3556000", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 2", "SAMEA5752541", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 8", "Sphere 2 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24", null, null, 6679993476.0, 87894651.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 8", "0:76", "A:3113787833;C:1255798935;G:1750515950;T:559763997;N:126761", 76, null, null, null, 3113787833, 1255798935, 1750515950, 559763997, 126761, "ERX3511271", "ERS3556000", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.66287, null, 0.41208, null, 0.99602, null, 0.17083, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9755, "ERR3489855", "ERX3511270", "ERS3556000", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 2", "SAMEA5752541", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 7", "Sphere 2 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 13238731764.0, 174193839.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 7", "0:76", "A:7630016769;C:1835321568;G:2775223283;T:997916159;N:253985", 76, null, null, null, 7630016769, 1835321568, 2775223283, 997916159, 253985, "ERX3511270", "ERS3556000", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.77269, null, 0.45994, null, 0.99683, null, 0.04249, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9756, "ERR3489854", "ERX3511269", "ERS3555999", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 1", "SAMEA5752540", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 6", "Sphere 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24", null, null, 3311799332.0, 43576307.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 6", "0:76", "A:1182325939;C:888677953;G:922571204;T:318159754;N:64482", 76, null, null, null, 1182325939, 888677953, 922571204, 318159754, 64482, "ERX3511269", "ERS3555999", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.57505, null, 0.24459, null, 0.99582, null, 0.43365, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9757, "ERR3489853", "ERX3511268", "ERS3555999", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "Sphere 1", "SAMEA5752540", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 5", "Sphere 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 7403181508.0, 97410283.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 5", "0:76", "A:4338227974;C:1233250165;G:1372229712;T:459322295;N:151362", 76, null, null, null, 4338227974, 1233250165, 1372229712, 459322295, 151362, "ERX3511268", "ERS3555999", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.765, null, 0.44747, null, 0.99515, null, 0.12467, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [9758, "ERR3489852", "ERX3511267", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 4", "64 cell 2 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 11722578884.0, 154244459.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 4", "0:76", "A:8175036829;C:1396062240;G:1882846539;T:268587131;N:46145", 76, null, null, null, 8175036829, 1396062240, 1882846539, 268587131, 46145, "ERX3511267", "ERS3555998", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.81133, null, 0.41331, null, 0.99823, null, 0.03453, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9759, "ERR3489851", "ERX3511266", "ERS3555998", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 2", "SAMEA5752539", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3", "64 cell 2 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 9525478088.0, 125335238.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 3", "0:76", "A:4813606784;C:2048902072;G:2140220088;T:522714000;N:35144", 76, null, null, null, 4813606784, 2048902072, 2140220088, 522714000, 35144, "ERX3511266", "ERS3555998", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.59747, null, 0.26784, null, 0.996, null, 0.21193, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9760, "ERR3489850", "ERX3511265", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3511265", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34707, null, 0.02129, null, 0.99797, null, 0.62478, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9761, "ERR3489849", "ERX3511264", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22", "run7_64_cell_SSU_12_13_14.fastq.gz", "fastq", 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 1", "0:76 1:0", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, 0, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3511264", "ERS3555997", "ERA2100634", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06893, null, 0.02559, null, 0.99766, null, 0.90567, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9762, "ERR3413870", "ERX3437516", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2", "64 cell 1 LSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 8544157652.0, 112423127.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 2", "0:76", "A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086", 76, null, null, null, 2633354802, 2582123846, 2505786164, 822713754, 179086, "ERX3437516", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.34696, null, 0.02086, null, 0.99795, null, 0.66261, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [9763, "ERR3413869", "ERX3437515", "ERS3555997", "ERP116106", "PRJEB33323", "Deconstructing the individual steps of vertebrate translation initiation", "ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422", "Other", "In eukaryotes  the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA  their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1  but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning  initiating  elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish  which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment  scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally  we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, "64 cell 1", "SAMEA5752538", "Computational Biology Unit", "ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1", "64 cell 1 SSU", "None", "RCP seq", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP116106", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03", null, null, 10139466432.0, 133414032.0, "ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 1", "0:76", "A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884", 76, null, null, null, 4628193785, 2494821868, 2485640988, 530605907, 203884, "ERX3437515", "ERS3555997", "ERA2028987", "Computational Biology Unit|European Nucleotide Archive", "Computational Biology Unit", 1, 0.06884, null, 0.02526, null, 0.99762, null, 0.89856, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-03", "Cleavage", "Embryo", "Undetermined", "Embryo Imprecise"], [10214, "ERR6617900", "ERX6244443", "ERS7291130", "ERP131213", "PRJEB46978", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing", "ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159", "Other", "Nano3P seq is a simple and robust method to accurately estimate transcript levels  tail lengths and tail nucleotide composition information in full length individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", null, "PolyA selected dRNA sequenced zebrafish 4hpf RNA", "Zebrafish 4hpf dRNA", "SAMEA9568396", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2023 12 28T01:07:30Z|ENA LAST UPDATE:2023 12 28T01:07:30Z|External Id:SAMEA9568396|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:30Z|INSDC last update:2023 12 28T01:07:30Z|INSDC status:public|Submitter Id:Zebrafish 4hpf dRNA1|common name:zebrafish|sample name:Zebrafish 4hpf dRNA1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1", "dRNA Zebrafish", "Direct RNA Sequencing", "Direct RNA Sequencing", null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP131213", "MinION sequencing", "ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28", "Zebrafish_4hpf_dRNA.fast5.tar.gz", "nanopore", 772304625.0, 897768.0, "ena RUN CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1", "0:860.25", "A:224977035;C:165273397;G:156659356;T:225394837;N:0", 860, null, null, null, 224977035, 165273397, 156659356, 225394837, 0, "ERX6244443", "ERS7291130", "ERA5995143", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.5, null, 0.0, null, 0.99997, null, 1.0, null, 962, null, "T", null, "long read", "ont", "ont", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2023-12-28", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [11042, "ERR9839781", "ERX9385638", "ERS12199238", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep3", "SAMEA110100413", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817", "cDNA897892 ZFRDR3", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA897892_ZFRDR3.tar.gz", "nanopore", 848659575.0, 587586.0, "ena RUN TAB 13 06 2022 16:07:52:808 818", "0:1444.32", "A:210205014;C:186527780;G:188214279;T:263712502;N:0", 1444, null, null, null, 210205014, 186527780, 188214279, 263712502, 0, "ERX9385638", "ERS12199238", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11043, "ERR9839780", "ERX9385637", "ERS12199237", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep2", "SAMEA110100412", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815", "cDNA123791 ZFRDR2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA123791_ZFRDR2.tar.gz", "nanopore", 2229275175.0, 1955617.0, "ena RUN TAB 13 06 2022 16:07:52:807 816", "0:1139.93", "A:533543922;C:498938137;G:515833119;T:680959997;N:0", 1139, null, null, null, 533543922, 498938137, 515833119, 680959997, 0, "ERX9385637", "ERS12199237", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11044, "ERR9839779", "ERX9385636", "ERS12199236", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish Ribodepleted RNA 2hpf  4hpf  6hpf", "Zebrafish Ribodepleted Rep1", "SAMEA110100411", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813", "cDNA786327 ZFRDR1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA786327_ZFRDR1.tar.gz", "nanopore", 1900613556.0, 1660167.0, "ena RUN TAB 13 06 2022 16:07:52:807 814", "0:1144.83", "A:473050820;C:438054520;G:425169743;T:564338473;N:0", 1144, null, null, null, 473050820, 438054520, 425169743, 564338473, 0, "ERX9385636", "ERS12199236", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Multi-stage", "Embryo", "Undetermined", "Embryo Imprecise"], [11045, "ERR9839778", "ERX9385635", "ERS12199235", "ERP138294", "PRJEB53494", "Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing", "94bf5509-4622-4d5f-b7c5-6a14bdfac340", "Other", "RNA polyadenylation plays a central role in RNA maturation  fate  and stability. In response to developmental cues  polyA tail lengths can vary  affecting the translation efficiency and stability of mRNAs. Here  we develop Nanopore three prime end capture sequencing Nano3P seq  a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance  tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol  Nano3P seq can sequence any given RNA molecule from its three prime end  regardless of its polyadenylation status  without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes  providing quantitative estimates of RNA abundance and tail lengths in mRNA  lncRNA  sn/snoRNA  scaRNA  and rRNA molecules. We find that  in addition to mRNA and lncRNA  polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover  we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level  correlating with mRNA decay. Finally  we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis.  Overall  Nano3P seq is a simple and robust method for accurately estimating transcript levels  tail lengths  and tail composition heterogeneity in individual reads  with minimal library preparation biases  both in the coding and non coding transcriptome.", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", null, "Zebrafish PolyA Selected RNA 4hpf", "Zebrafish pA selected", "SAMEA110100410", "CENTER FOR GENOMIC REGULATION (CRG)", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100410|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish pA selected|common name:zebrafish|sample name:Zebrafish pA selected", null, null, null, null, null, null, null, null, "MinION sequencing", "ena EXPERIMENT TAB 13 06 2022 16:07:52:807 811", "cDNA852361 ZFPA4R1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "OXFORD_NANOPORE", "MinION", null, "ERP138294", "MinION sequencing", "ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10", "cDNA852361_ZFPA4R1.tar.gz", "nanopore", 348224822.0, 233101.0, "ena RUN TAB 13 06 2022 16:07:52:807 812", "0:1493.88", "A:88963756;C:76104775;G:73909507;T:109246784;N:0", 1493, null, null, null, 88963756, 76104775, 73909507, 109246784, 0, "ERX9385635", "ERS12199235", "ERA15547404", "CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive", "CENTER FOR GENOMIC REGULATION (CRG)", 1, 0.34147, null, 0.26829, null, 0.99993, null, 0.16666, null, 1537, null, "T", null, "long read", "ont", "ont", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2022-10-10", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [25295, "SRR25764045", "SRX21486723", "SRS18719024", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf Ribo seq rep1", "GSM7734770", null, "source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT bud 10 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al.  2013] the following options:   outFilterMultimapNmax 1   seedSearchStartLmax 15   outSAMtype BAM SortedByCoordinate   outFilterMismatchNmax 2   alignEndsType EndToEnd   quantMode TranscriptomeSAM   outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Gastrula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG", "GSM7734770", "GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734770 r1", "GSM7734770", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_bud_1.fastq.gz", "fastq", 1476985703.0, 55745002.0, "GSM7734770 r1", "0:26.50", "A:266369385;C:466461341;G:473469631;T:270671671;N:13675", 26, null, null, null, 266369385, 466461341, 473469631, 270671671, 13675, "SRX21486723", "SRS18719024", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.773, null, 0.14121, null, 0.82242, null, 0.78464, null, 30, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25296, "SRR25764046", "SRX21486722", "SRS18719023", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf Ribo seq rep1", "GSM7734769", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT sphere 4 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al.  2013] the following options:   outFilterMultimapNmax 1   seedSearchStartLmax 15   outSAMtype BAM SortedByCoordinate   outFilterMismatchNmax 2   alignEndsType EndToEnd   quantMode TranscriptomeSAM   outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG", "GSM7734769", "GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734769 r1", "GSM7734769", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_sphere_1.fastq.gz", "fastq", 1336027898.0, 47907512.0, "GSM7734769 r1", "0:27.89", "A:229038284;C:439455963;G:429428292;T:238088512;N:16847", 27, null, null, null, 229038284, 439455963, 429428292, 238088512, 16847, "SRX21486722", "SRS18719023", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.85867, null, 0.20418, null, 0.8776, null, 0.79481, null, 24, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [30658, "SRR28054753", "SRX23704452", "SRS20534448", "SRP491086", "PRJNA1078753", "Integrated mRNA  and miRNA  sequencing analyses unveil the underlying mechanism of tobacco pollutant induced developmental toxicity in zebrafish embryos", "PRJNA1078753", "Other", "Tobacco pollutants are prevalent in the environment  leading to inadvertent exposure of pregnant females. Studies of these pollutants' toxic effects on development have not fully elucidated the potential underlying mechanisms. Therefore  in this study  we aim at investigate the developmental toxicity induced by cigarette smoke extract CSE at concentrations of 0.25%  1%  and 2.5% using a zebrafish embryo toxicity test and integrated transcriptomic analysis of microRNA miRNA and messenger RNA mRNA. The findings revealed that CSE caused developmental toxicity  including increased mortality and decreased incubation rate  in a dose dependent manner. Moreover  CSE induced malformations and apoptosis  specifically in the head and heart of zebrafish larvae. We used mRNA and miRNA sequencing analyses to compare changes in the expression of genes and miRNAs in zebrafish larvae. The bioinformatics analysis indicates that the mechanism underlying CSE induced developmental toxicity was associated with genetic repair impairment  apoptosis disorder  and lipid metabolism disturbance. The enrichment analysis and RT qPCR show that the ctsba gene plays a crucial function in embryo developmental apoptosis  and the fads2 gene mainly regulates lipid metabolic toxicity. The results of this study improve the understanding of CSE induced developmental toxicity in zebrafish embryos and contribute insights into the formulation of novel preventive strategies against tobacco pollutants during early embryonic development.", null, null, null, null, "S21K1230", null, "library ID:H 3|title:High 3|library strategy:OTHER|library source:METATRANSCRIPTIOMIC|library selection:other|library layout:paired|platform:ILLUMINA|instrument model:RNA seq|filetype:fastq|filename:S21K1230 rep1 1 URNA S74 L003 R1 001.fastq|filename2:S21K1230 rep1 1 URNA S74 L003 R2 001.fastq|host:missing|isolation source:missing|collection date:missing|geographic location:missing|latitude and longitude:missing|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "High 3", "H 3", "H 3", "missing", null, null, "RNA-Seq", "METATRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP491086", null, null, "S21K1230_rep1_1_URNA_S74_L003_R1_001.fastq.gz S21K1230_rep1_1_URNA_S74_L003_R2_001.fastq.gz", "fastq fastq", 6117817800.0, 20392726.0, "S21K1230 rep1 1 URNA S74 L003 R1 001.fastq.gz", "0:150 1:150", "A:1635728688;C:1405168032;G:1464072107;T:1612834762;N:14211", 150, 150, null, null, 1635728688, 1405168032, 1464072107, 1612834762, 14211, "SRX23704452", "SRS20534448", "SRA1806456", "The Second Affiliated Hospital of Shantou University Medical College|Department of Burns and Plastic Surgery", "The Second Affiliated Hospital of Shantou University Medical College", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-22", "Undetermined", "Multi-stage", "Undetermined", "Undetermined"], [36053, "SRR33444765", "SRX28685529", "SRS24952431", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "1 8 dimethylnaphthalene  A", "GSM8969898", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:1 8 dimethylnaphthalene|batch:1|geo loc name:missing|collection date:missing", "1 8 dimethylnaphthalene  A", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:1 8 dimethylnaphthalene|batch:1", "GSM8969898", "GSM8969898: 1 8 dimethylnaphthalene  A; Danio rerio; OTHER", "GSM8969898 r1", "GSM8969898", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "2_A.fastq.gz", "fastq", 610412472.0, 11968872.0, "GSM8969898 r1", "0:51", "A:127080561;C:159924680;G:139627579;T:183641966;N:137686", 51, null, null, null, 127080561, 159924680, 139627579, 183641966, 137686, "SRX28685529", "SRS24952431", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36054, "SRR33444766", "SRX28685528", "SRS24952432", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 2  C", "GSM8969935", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2|geo loc name:missing|collection date:missing", "control day 2  C", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2", "GSM8969935", "GSM8969935: control day 2  C; Danio rerio; OTHER", "GSM8969935 r1", "GSM8969935", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C2C.fastq.gz", "fastq", 741413877.0, 14537527.0, "GSM8969935 r1", "0:51", "A:153346994;C:193370788;G:172893997;T:221634171;N:167927", 51, null, null, null, 153346994, 193370788, 172893997, 221634171, 167927, "SRX28685528", "SRS24952432", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36055, "SRR33444767", "SRX28685527", "SRS24952430", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 2  B", "GSM8969934", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2|geo loc name:missing|collection date:missing", "control day 2  B", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2", "GSM8969934", "GSM8969934: control day 2  B; Danio rerio; OTHER", "GSM8969934 r1", "GSM8969934", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C2B.fastq.gz", "fastq", 541591338.0, 10619438.0, "GSM8969934 r1", "0:51", "A:110558693;C:142536702;G:127264949;T:161109133;N:121861", 51, null, null, null, 110558693, 142536702, 127264949, 161109133, 121861, "SRX28685527", "SRS24952430", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36056, "SRR33444768", "SRX28685526", "SRS24952429", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 2  A", "GSM8969933", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2|geo loc name:missing|collection date:missing", "control day 2  A", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 2|batch:2", "GSM8969933", "GSM8969933: control day 2  A; Danio rerio; OTHER", "GSM8969933 r1", "GSM8969933", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C2A.fastq.gz", "fastq", 613454112.0, 12028512.0, "GSM8969933 r1", "0:51", "A:125133985;C:160879875;G:143614243;T:183687282;N:138727", 51, null, null, null, 125133985, 160879875, 143614243, 183687282, 138727, "SRX28685526", "SRS24952429", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36057, "SRR33444769", "SRX28685525", "SRS24952428", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 1  C", "GSM8969932", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1|geo loc name:missing|collection date:missing", "control day 1  C", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1", "GSM8969932", "GSM8969932: control day 1  C; Danio rerio; OTHER", "GSM8969932 r1", "GSM8969932", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C1C.fastq.gz", "fastq", 474767415.0, 9309165.0, "GSM8969932 r1", "0:51", "A:97071261;C:124093451;G:110241992;T:143253948;N:106763", 51, null, null, null, 97071261, 124093451, 110241992, 143253948, 106763, "SRX28685525", "SRS24952428", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36058, "SRR33444770", "SRX28685524", "SRS24952427", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 1  B", "GSM8969931", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1|geo loc name:missing|collection date:missing", "control day 1  B", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1", "GSM8969931", "GSM8969931: control day 1  B; Danio rerio; OTHER", "GSM8969931 r1", "GSM8969931", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C1B.fastq.gz", "fastq", 457427772.0, 8969172.0, "GSM8969931 r1", "0:51", "A:94621194;C:123105730;G:103779476;T:135818957;N:102415", 51, null, null, null, 94621194, 123105730, 103779476, 135818957, 102415, "SRX28685524", "SRS24952427", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36059, "SRR33444771", "SRX28685523", "SRS24952426", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "control day 1  A", "GSM8969930", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1|geo loc name:missing|collection date:missing", "control day 1  A", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:control day 1|batch:1", "GSM8969930", "GSM8969930: control day 1  A; Danio rerio; OTHER", "GSM8969930 r1", "GSM8969930", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "C1A.fastq.gz", "fastq", 492735021.0, 9661471.0, "GSM8969930 r1", "0:51", "A:101186692;C:127371147;G:115048213;T:149017307;N:111662", 51, null, null, null, 101186692, 127371147, 115048213, 149017307, 111662, "SRX28685523", "SRS24952426", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36060, "SRR33444772", "SRX28685522", "SRS24952423", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "1 6 7 trimethylnaphthalene  E", "GSM8969929", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1|geo loc name:missing|collection date:missing", "1 6 7 trimethylnaphthalene  E", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1", "GSM8969929", "GSM8969929: 1 6 7 trimethylnaphthalene  E; Danio rerio; OTHER", "GSM8969929 r1", "GSM8969929", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "9_E.fastq.gz", "fastq", 611528913.0, 11990763.0, "GSM8969929 r1", "0:51", "A:124350552;C:160747373;G:139974969;T:186316449;N:139570", 51, null, null, null, 124350552, 160747373, 139974969, 186316449, 139570, "SRX28685522", "SRS24952423", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36061, "SRR33444773", "SRX28685521", "SRS24952425", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "1 6 7 trimethylnaphthalene  D", "GSM8969928", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1|geo loc name:missing|collection date:missing", "1 6 7 trimethylnaphthalene  D", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1", "GSM8969928", "GSM8969928: 1 6 7 trimethylnaphthalene  D; Danio rerio; OTHER", "GSM8969928 r1", "GSM8969928", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "9_D.fastq.gz", "fastq", 628858662.0, 12330562.0, "GSM8969928 r1", "0:51", "A:128538964;C:164901356;G:144434115;T:190840964;N:143263", 51, null, null, null, 128538964, 164901356, 144434115, 190840964, 143263, "SRX28685521", "SRS24952425", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [36062, "SRR33444774", "SRX28685520", "SRS24952424", "SRP583274", "PRJNA1259243", "Structure Dependent Developmental Toxicity of Alkyl Substituted Naphthalenes", "GSE296410", "Transcriptome Analysis", "Naphthalene and its alkyl substituted derivatives are among the most abundant polycyclic aromatic hydrocarbons PAHs in environmental and human exposure studies  yet their developmental toxicity and mode of action remain poorly understood due to challenges in testing of semi volatile compounds. This study developed a vial based high through put method to effectively assess the activity of naphthalenes and a set of 24 alkyl substituted naphthalenes. Early life stage zebrafish were exposed to a concentration series of each chemical 0 50 \u00b5M in rotating sealed glass vials to minimize volatilization. Benchmark concentration BMC50 values were calculated for morphological endpoints and lowest effect levels were determined for behavioral effects. The data were assessed for evidence of a narcotic mode of action using body burden measurements for select chemicals and logKow modeling. Targeted transcriptomics at a single concentration and timepoint as well as in silico molecular docking were conducted to generate mode of action hypothesis. The vial method enabled detection of highly variable developmental toxicity not previously observed using standard 96 well plate exposures. LogKow and body burden were poor predictors of toxicity  suggesting a non narcotic mode of action. Transcriptomic analysis revealed a limited but notable set of differentially expressed genes  with evidence for the disruption of glucocorticoid signaling pathways. Molecular docking identified potential protein targets e.g.  CYP1A2  NT5E  FOLR1 that may mediate observed effects. This study demonstrates the importance of appropriate exposure methods for semi volatile compounds  reveals structure dependent toxicity among alkyl substituted naphthalenes  and provides a foundation for further mechanistic studies and improved risk assessment of alkyl substituted PAHs. Overall design: Zebrafish were exposed to 25 chemicals  naphthalene and 24 alkyl sustituted naphthalenes  using a vial exposure method. Embryos were exposed to 20 uM of each chemical in groups of 8 in 2 mL of media in 2 mL glass vials from xxx hpf ttwo xxx hpf. RNA was collected at at 48 hpf. Exposures  collections and extractions were conducted over two days. Targeted transcriptomics was preformed using the TempO seq platform.", null, null, null, "1 6 7 trimethylnaphthalene  B", "GSM8969927", null, "source name:whole animal|tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1|geo loc name:missing|collection date:missing", "1 6 7 trimethylnaphthalene  B", "Demultiplexing and alignment was performed using the manufacture provided processing platform TempO SeqR BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Principal component analysis PCA of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day nested by experimental design. At this time one control sample  control day1  B was identified as an outlier and removed from all future analysis. The batch effect was removed from unnormalized data using the ComBat seq function from the SVA R package Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor. Assembly: GRCz11 Supplementary files format and content: .csv file containing raw count data Supplementary files format and content: .csv file containing batch corrected and normalized data", "whole animal", "When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute  then transferred to a 0.5% sodium chloride solution for 5 minutes  then transferred to a    % sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 \u00b5M using DMSO. 10 \u00b5L of diluted chemical stock was added to each vial  vials were immediately capped and inverted 3 times to ensure mixing  no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28\u00b0C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96 well plates loaded with 100 \u00b5L clean EM. At 48 hpf embryos were collected for RNA extraction  embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells  6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes  placed on ice 30 sec  excess media removed  placed back on ice 30 sec  and 200 \u00b5L RNA shield added. Five pooled samples were collected from each treatment.", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer\u2019s instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "tissue:whole animal|genotype:5D WT|treatment:1 6 7 trimethylnaphthalene|batch:1", "GSM8969927", "GSM8969927: 1 6 7 trimethylnaphthalene  B; Danio rerio; OTHER", "GSM8969927 r1", "GSM8969927", "1", "1mL of 1\u00b5m beads and 500\u00b5L of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100\u00b5L of lysis buffer was added to tube containing pooled embryo samples and 200\u00b5L of RNA shield  the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 \u00b5L of the supernatant was then transferred to two plates containing 275\u00b5L of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample  post series of washes the RNA is eluted in 50\u00b5Lof ultra pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate  samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4 5 viable RNA extraction replicates  for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/\u00b5L. 1 \u00b5L per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96 sample TempO Seq S1500 + Zebrafish Surrogate Assay panel BioSpyder Technologies  Inc.  Carlsbad  CA  United States. Briefly  samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos  digestion  and ligation. Proper amplification was verified using real time PCR green fluorescence. Library purification was performed using the Macherey Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer's instructions. PCR amplification products were pooled into a single sequencing library 5 \u00b5L each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell BioSpyder Technologies  Inc.  Carlsbad  CA  United States.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq X", null, "SRP583274", null, null, "9_B.fastq.gz", "fastq", 550098036.0, 10786236.0, "GSM8969927 r1", "0:51", "A:112188300;C:144676062;G:126419391;T:166689819;N:124464", 51, null, null, null, 112188300, 144676062, 126419391, 166689819, 124464, "SRX28685520", "SRS24952424", "SRA2124446", "SARL, Environmental and Molecular Toxicology, Oregon State University", "SARL, Environmental and Molecular Toxicology, Oregon State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-05-06", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 550, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"technology\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "other", "p2": "unknown"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown", "results": [{"value": "OTHER", "label": "OTHER", "count": 297, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_strategy=OTHER", "selected": false}, {"value": "RNA-Seq", "label": "RNA-Seq", "count": 156, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "RIP-Seq", "label": "RIP-Seq", "count": 43, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_strategy=RIP-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 549, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "METATRANSCRIPTOMIC", "label": "METATRANSCRIPTOMIC", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown&experiment.library_source=METATRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=unknown", "results": 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