{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.platform = \"ILLUMINA\" and tissue_curation_coarse = \"Embryo Imprecise\"", "rows": [[9717, "ERR3842002", "ERX3854564", "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. 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. 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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, "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"], [29719, "SRR27485664", "SRX23156885", "SRS20107306", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs R3", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: eggs  rep4", "EV06009", "EV06009", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06009.R1.fastq.gz", "fastq", 809138488.0, 10734286.0, "EV06009.R1.fastq.gz", "0:75.38", "A:236901398;C:156814193;G:179647937;T:235732894;N:42066", 75, null, null, null, 236901398, 156814193, 179647937, 235732894, 42066, "SRX23156885", "SRS20107306", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.92159, null, 0.07516, null, 0.837, null, 0.7566, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29730, "SRR27485675", "SRX23156874", "SRS20107295", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: eggs  rep4", "EV06002", "EV06002", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. 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Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV06002.R1.fastq.gz", "fastq", 632849068.0, 8404028.0, "EV06002.R1.fastq.gz", "0:75.30", "A:194183801;C:123105421;G:139266843;T:176255048;N:37955", 75, null, null, null, 194183801, 123105421, 139266843, 176255048, 37955, "SRX23156874", "SRS20107295", "SRA1783314", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.88896, null, 0.09385, null, 0.81864, null, 0.73385, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-11", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29737, "SRR27477297", "SRX23148650", "SRS20099368", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "mRNA seq of zebrafish: eggs  rep4", "EV09002", "EV09002", "RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV09002.R1.fastq.gz", "fastq", 546999929.0, 7270092.0, "EV09002.R1.fastq.gz", "0:75.24", "A:165415993;C:110874896;G:124384517;T:146294099;N:30424", 75, null, null, null, 165415993, 110874896, 124384517, 146294099, 30424, "SRX23148650", "SRS20099368", "SRA1782413", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.9065, null, 0.11883, null, 0.82231, null, 0.74466, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "poly_a", "lexogen", "bulk", "unknown", "unknown", null, "Austria", "2024-01-10", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29745, "SRR27467678", "SRX23139228", "SRS20090268", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs mock R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  mock  rep2", "EV04001", "EV04001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04001.R1.fastq.gz", "fastq", 970037880.0, 6928842.0, "EV04001.R1.fastq.gz", "0:140", "A:258735538;C:237798398;G:268588390;T:204871983;N:43571", 140, null, null, null, 258735538, 237798398, 268588390, 204871983, 43571, "SRX23139228", "SRS20090268", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29761, "SRR27437481", "SRX23109816", "SRS20064569", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  BS  rep3", "EV07003", "EV07003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07003.R1.fastq.gz", "fastq", 688960160.0, 4921144.0, "EV07003.R1.fastq.gz", "0:140", "A:187831021;C:119362814;G:195214528;T:186533242;N:18555", 140, null, null, null, 187831021, 119362814, 195214528, 186533242, 18555, "SRX23109816", "SRS20064569", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29762, "SRR27437482", "SRX23109815", "SRS20064568", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  DM  rep3", "EV07002", "EV07002", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07002.R1.fastq.gz", "fastq", 520725380.0, 3719467.0, "EV07002.R1.fastq.gz", "0:140", "A:138972126;C:125739732;G:142785467;T:113214166;N:13889", 140, null, null, null, 138972126, 125739732, 142785467, 113214166, 13889, "SRX23109815", "SRS20064568", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00014, null, 1e-05, null, 0.99969, null, 0.5, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29763, "SRR27437483", "SRX23109814", "SRS20064570", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  mock  rep3", "EV07001", "EV07001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV07001.R1.fastq.gz", "fastq", 684538960.0, 4889564.0, "EV07001.R1.fastq.gz", "0:140", "A:178906891;C:169237174;G:192342342;T:144034095;N:18458", 140, null, null, null, 178906891, 169237174, 192342342, 144034095, 18458, "SRX23109814", "SRS20064570", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0001, null, 1e-05, null, 0.99977, null, 0.76923, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29782, "SRR27435867", "SRX23108229", "SRS20063067", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs BS R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  BS  rep4", "EV08006", "EV08006", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08006.R1.fastq.gz", "fastq", 501745580.0, 3583897.0, "EV08006.R1.fastq.gz", "0:140", "A:124242793;C:76040623;G:131428076;T:170000220;N:33868", 140, null, null, null, 124242793, 76040623, 131428076, 170000220, 33868, "SRX23108229", "SRS20063067", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 4e-05, null, 0.0, null, 0.99993, null, 0.66666, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29783, "SRR27435868", "SRX23108228", "SRS20063063", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs DM R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  DM  rep4", "EV08005", "EV08005", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08005.R1.fastq.gz", "fastq", 740147520.0, 5286768.0, "EV08005.R1.fastq.gz", "0:140", "A:192131338;C:198130943;G:182616631;T:167216834;N:51774", 140, null, null, null, 192131338, 198130943, 182616631, 167216834, 51774, "SRX23108228", "SRS20063063", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00052, null, 8e-05, null, 0.99922, null, 0.92537, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29784, "SRR27435869", "SRX23108227", "SRS20063065", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "eggs mock R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: eggs  mock  rep4", "EV08004", "EV08004", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08004.R1.fastq.gz", "fastq", 761663140.0, 5440451.0, "EV08004.R1.fastq.gz", "0:140", "A:194684966;C:192212418;G:196372829;T:178340184;N:52743", 140, null, null, null, 194684966, 192212418, 196372829, 178340184, 52743, "SRX23108227", "SRS20063065", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00151, null, 0.00037, null, 0.99884, null, 0.82352, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [36423, "SRR516547", "SRX156325", "SRS347201", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   fertilized egg", "D. rerio fertilized egg", "D. rerio fertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio fertilized egg", "CAGE   D. rerio fertilized egg", "D. rerio fertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "CAGE_fertilized_egg.fastq", "fastq", 160948350.0, 5961050.0, "CAGE   D. rerio fertilized egg", "0:27", "A:42030009;C:34700589;G:45399755;T:38817997;N:0", 27, null, null, null, 42030009, 34700589, 45399755, 38817997, 0, "SRX156325", "SRS347201", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.49394, null, 0.07554, null, 0.81684, null, 0.79759, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [36666, "SRR800043", "SRX257153", "SRS405345", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq totalRNARibominus", "sphere RNAseq totalRNARibominus", "7986X2", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP020008", null, null, "sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz", "Illumina native", 3029181300.0, 60583626.0, "7986X2 110510 SN141 0338 AB06MWABXX 7", "0:50", "A:768949744;C:733340278;G:903149841;T:623482299;N:259138", 50, null, null, null, 768949744, 733340278, 903149841, 623482299, 259138, "SRX257153", "SRS405345", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.83515, null, 0.15524, null, 0.81209, null, 0.81031, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [36667, "SRR800044", "SRX257153", "SRS405345", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq totalRNARibominus", "sphere RNAseq totalRNARibominus", "7986X2", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP020008", null, null, "sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz", "Illumina native", 3947123500.0, 78942470.0, "7986X2 110606 SN141 0359 BD0D8KABXX 6", "0:50", "A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861", 50, null, null, null, 1000468440, 957437794, 1171831772, 817292633, 92861, "SRX257153", "SRS405345", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.81283, null, 0.14906, null, 0.81335, null, 0.81698, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [36668, "SRR800037", "SRX257149", "SRS405106", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "egg RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg", null, null, null, null, null, null, null, null, "egg RNAseq totalRNARibominus", "egg RNAseq totalRNARibominus", "7784X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP020008", null, null, null, null, 3584440000.0, 71688800.0, "7784X1 110323 SN141 0332 A81FDVABXX 8", "0:50", "A:1013532157;C:812179975;G:992916103;T:765761452;N:50313", 50, null, null, null, 1013532157, 812179975, 992916103, 765761452, 50313, "SRX257149", "SRS405106", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.87304, null, 0.12853, null, 0.81988, null, 0.80407, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [36669, "SRR800038", "SRX257149", "SRS405106", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "egg RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg", null, null, null, null, null, null, null, null, "egg RNAseq totalRNARibominus", "egg RNAseq totalRNARibominus", "7784X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>", "SRP020008", null, null, null, null, 2794240450.0, 55884809.0, "7784X1 110119 SN141 0323 B8162JABXX 8", "0:50", "A:792200981;C:632130044;G:772351331;T:596980885;N:577209", 50, null, null, null, 792200981, 632130044, 772351331, 596980885, 577209, "SRX257149", "SRS405106", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.86104, null, 0.12909, null, 0.82266, null, 0.80894, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58479, "SRR12436783", "SRX8932472", "SRS7188817", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724702 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724702", null, null, "Ski7 FER R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB", "GSM4724702", "GSM4724702: Ski7 FER R3 polyA; Danio rerio; RNA Seq", "GSM4724702", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724702", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_FER_R3_polyA.fastq", "fastq", 1777842000.0, 17778420.0, "GSM4724702 r1", "0:100", "A:440367983;C:434184573;G:419300944;T:483847825;N:140675", 100, null, null, null, 440367983, 434184573, 419300944, 483847825, 140675, "SRX8932472", "SRS7188817", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96519, null, 0.0558, null, 0.79762, null, 0.49071, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58480, "SRR12436782", "SRX8932471", "SRS7188816", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724701 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724701", null, null, "Ski7 FER R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB", "GSM4724701", "GSM4724701: Ski7 FER R2 polyA; Danio rerio; RNA Seq", "GSM4724701", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724701", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_FER_R2_polyA.fastq", "fastq", 1580941100.0, 15809411.0, "GSM4724701 r1", "0:100", "A:393346905;C:386319994;G:375568338;T:425580399;N:125464", 100, null, null, null, 393346905, 386319994, 375568338, 425580399, 125464, "SRX8932471", "SRS7188816", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96387, null, 0.06115, null, 0.80251, null, 0.48311, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58481, "SRR12436781", "SRX8932470", "SRS7188815", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 FER R1 polyA", "GSM4724700", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB", "Ski7 FER R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB", "GSM4724700", "GSM4724700: Ski7 FER R1 polyA; Danio rerio; RNA Seq", "GSM4724700", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724700", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_FER_R1_polyA.fastq", "fastq", 2213300600.0, 22133006.0, "GSM4724700 r1", "0:100", "A:554108128;C:532528202;G:525489897;T:601097373;N:77000", 100, null, null, null, 554108128, 532528202, 525489897, 601097373, 77000, "SRX8932470", "SRS7188815", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96118, null, 0.06109, null, 0.8046, null, 0.48546, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58482, "SRR12436780", "SRX8932469", "SRS7188814", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 ACT R3 polyA", "GSM4724699", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "Ski7 ACT R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "GSM4724699", "GSM4724699: Ski7 ACT R3 polyA; Danio rerio; RNA Seq", "GSM4724699", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_ACT_R3_polyA.fastq", "fastq", 1922804200.0, 19228042.0, "GSM4724699 r1", "0:100", "A:480850703;C:463917366;G:452391538;T:525491911;N:152682", 100, null, null, null, 480850703, 463917366, 452391538, 525491911, 152682, "SRX8932469", "SRS7188814", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96391, null, 0.0566, null, 0.80046, null, 0.48338, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58483, "SRR12436779", "SRX8932468", "SRS7188813", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 ACT R2 polyA", "GSM4724698", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "Ski7 ACT R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "GSM4724698", "GSM4724698: Ski7 ACT R2 polyA; Danio rerio; RNA Seq", "GSM4724698", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724698", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_ACT_R2_polyA.fastq", "fastq", 1928647900.0, 19286479.0, "GSM4724698 r1", "0:100", "A:482751186;C:469163733;G:460738816;T:515841418;N:152747", 100, null, null, null, 482751186, 469163733, 460738816, 515841418, 152747, "SRX8932468", "SRS7188813", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96439, null, 0.05875, null, 0.80921, null, 0.47651, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58484, "SRR12436778", "SRX8932467", "SRS7188812", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 ACT R1 polyA", "GSM4724697", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "Ski7 ACT R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:activated egg|strain:TLAB", "GSM4724697", "GSM4724697: Ski7 ACT R1 polyA; Danio rerio; RNA Seq", "GSM4724697", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724697", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_ACT_R1_polyA.fastq", "fastq", 1459115400.0, 14591154.0, "GSM4724697 r1", "0:100", "A:361126428;C:358381337;G:346060607;T:393431535;N:115493", 100, null, null, null, 361126428, 358381337, 346060607, 393431535, 115493, "SRX8932467", "SRS7188812", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96515, null, 0.06732, null, 0.80395, null, 0.48544, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58485, "SRR12436777", "SRX8932466", "SRS7188811", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 INA R3 polyA", "GSM4724696", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "Ski7 INA R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "GSM4724696", "GSM4724696: Ski7 INA R3 polyA; Danio rerio; RNA Seq", "GSM4724696", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724696", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_SQU_R3_polyA.fastq", "fastq", 1063954100.0, 10639541.0, "GSM4724696 r1", "0:100", "A:265551085;C:258698639;G:249117151;T:290502423;N:84802", 100, null, null, null, 265551085, 258698639, 249117151, 290502423, 84802, "SRX8932466", "SRS7188811", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96171, null, 0.05846, null, 0.77346, null, 0.49713, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58486, "SRR12436776", "SRX8932465", "SRS7188810", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 INA R2 polyA", "GSM4724695", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "Ski7 INA R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "GSM4724695", "GSM4724695: Ski7 INA R2 polyA; Danio rerio; RNA Seq", "GSM4724695", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724695", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_SQU_R2_polyA.fastq", "fastq", 12041609400.0, 120416094.0, "GSM4724695 r1", "0:100", "A:3032420667;C:2912793806;G:2864619397;T:3231646175;N:129355", 100, null, null, null, 3032420667, 2912793806, 2864619397, 3231646175, 129355, "SRX8932465", "SRS7188810", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9612, null, 0.0577, null, 0.81091, null, 0.48028, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58487, "SRR12436775", "SRX8932464", "SRS7188809", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 INA R1 polyA", "GSM4724694", null, "tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "Ski7 INA R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:ski7 / |developmental stage:inactive egg|strain:TLAB", "GSM4724694", "GSM4724694: Ski7 INA R1 polyA; Danio rerio; RNA Seq", "GSM4724694", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724694", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "Ski7_Ooc_SQU_R1_polyA.fastq", "fastq", 1017000600.0, 10170006.0, "GSM4724694 r1", "0:100", "A:250669909;C:250298820;G:241072052;T:274878959;N:80860", 100, null, null, null, 250669909, 250298820, 241072052, 274878959, 80860, "SRX8932464", "SRS7188809", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96496, null, 0.05463, null, 0.80592, null, 0.47885, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58512, "SRR12436750", "SRX8932439", "SRS7188784", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT FER R3 polyA", "GSM4724669", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "WT FER R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "GSM4724669", "GSM4724669: WT FER R3 polyA; Danio rerio; RNA Seq", "GSM4724669", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724669", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_FER_R3_polyA.fastq", "fastq", 6771381900.0, 67713819.0, "GSM4724669 r1", "0:100", "A:1749508781;C:1638169429;G:1570468624;T:1813188646;N:46420", 100, null, null, null, 1749508781, 1638169429, 1570468624, 1813188646, 46420, "SRX8932439", "SRS7188784", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96178, null, 0.0557, null, 0.8254, null, 0.49638, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58513, "SRR12436749", "SRX8932438", "SRS7188783", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT FER R2 polyA", "GSM4724668", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "WT FER R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "GSM4724668", "GSM4724668: WT FER R2 polyA; Danio rerio; RNA Seq", "GSM4724668", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724668", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_FER_R2_polyA.fastq", "fastq", 1061307000.0, 10613070.0, "GSM4724668 r1", "0:100", "A:257645591;C:262618152;G:256246632;T:284713098;N:83527", 100, null, null, null, 257645591, 262618152, 256246632, 284713098, 83527, "SRX8932438", "SRS7188783", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.97035, null, 0.03791, null, 0.81769, null, 0.49181, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58514, "SRR12436748", "SRX8932437", "SRS7188782", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT FER R1 polyA", "GSM4724667", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "WT FER R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:fertilized egg|strain:TLAB", "GSM4724667", "GSM4724667: WT FER R1 polyA; Danio rerio; RNA Seq", "GSM4724667", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724667", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_FER_R1_polyA.fastq", "fastq", 1139600300.0, 11396003.0, "GSM4724667 r1", "0:100", "A:278063418;C:281065192;G:275555423;T:304826973;N:89294", 100, null, null, null, 278063418, 281065192, 275555423, 304826973, 89294, "SRX8932437", "SRS7188782", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96734, null, 0.06497, null, 0.81515, null, 0.49598, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58515, "SRR12436747", "SRX8932436", "SRS7188781", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT ACT R3 polyA", "GSM4724666", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB", "WT ACT R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:activated egg|strain:TLAB", "GSM4724666", "GSM4724666: WT ACT R3 polyA; Danio rerio; RNA Seq", "GSM4724666", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724666", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_ACT_R3_polyA.fastq", "fastq", 8285065900.0, 82850659.0, "GSM4724666 r1", "0:100", "A:2144352935;C:1997916723;G:1922332681;T:2220387512;N:76049", 100, null, null, null, 2144352935, 1997916723, 1922332681, 2220387512, 76049, "SRX8932436", "SRS7188781", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96318, null, 0.06182, null, 0.82511, null, 0.49104, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58516, "SRR12436746", "SRX8932435", "SRS7188780", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT ACT R2 polyA", "GSM4724665", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB", "WT ACT R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:activated egg|strain:TLAB", "GSM4724665", "GSM4724665: WT ACT R2 polyA; Danio rerio; RNA Seq", "GSM4724665", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724665", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_ACT_R2_polyA.fastq", "fastq", 1209882800.0, 12098828.0, "GSM4724665 r1", "0:100", "A:302800050;C:293974175;G:286616960;T:326395031;N:96584", 100, null, null, null, 302800050, 293974175, 286616960, 326395031, 96584, "SRX8932435", "SRS7188780", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96659, null, 0.054, null, 0.81694, null, 0.49155, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58517, "SRR12436745", "SRX8932434", "SRS7188779", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT ACT R1 polyA", "GSM4724664", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB", "WT ACT R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:activated egg|strain:TLAB", "GSM4724664", "GSM4724664: WT ACT R1 polyA; Danio rerio; RNA Seq", "GSM4724664", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724664", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_ACT_R1_polyA.fastq", "fastq", 1664829900.0, 16648299.0, "GSM4724664 r1", "0:100", "A:407654756;C:407749206;G:401595821;T:447697470;N:132647", 100, null, null, null, 407654756, 407749206, 401595821, 447697470, 132647, "SRX8932434", "SRS7188779", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96622, null, 0.06206, null, 0.81477, null, 0.49247, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58518, "SRR12436744", "SRX8932433", "SRS7188778", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT INA R3 polyA", "GSM4724663", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB", "WT INA R3 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:inactive egg|strain:TLAB", "GSM4724663", "GSM4724663: WT INA R3 polyA; Danio rerio; RNA Seq", "GSM4724663", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724663", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_SQU_R3_polyA.fastq", "fastq", 7170278200.0, 71702782.0, "GSM4724663 r1", "0:100", "A:1852022154;C:1727198429;G:1664295627;T:1926714520;N:47470", 100, null, null, null, 1852022154, 1727198429, 1664295627, 1926714520, 47470, "SRX8932433", "SRS7188778", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96163, null, 0.06005, null, 0.81686, null, 0.48888, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58519, "SRR12436743", "SRX8932432", "SRS7188777", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT INA R2 polyA", "GSM4724662", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB", "WT INA R2 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:inactive egg|strain:TLAB", "GSM4724662", "GSM4724662: WT INA R2 polyA; Danio rerio; RNA Seq", "GSM4724662", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724662", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_SQU_R2_polyA.fastq", "fastq", 3912697500.0, 39126975.0, "GSM4724662 r1", "0:100", "A:975441132;C:951912258;G:931850781;T:1053181584;N:311745", 100, null, null, null, 975441132, 951912258, 931850781, 1053181584, 311745, "SRX8932432", "SRS7188777", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96632, null, 0.05261, null, 0.80685, null, 0.49154, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [58520, "SRR12436742", "SRX8932431", "SRS7188776", "SRP253077", "PRJNA613025", "Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition", "GSE147112", "Transcriptome Analysis", "Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition  which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions  changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified  it remains unclear which cellular machineries contribute to remodeling  the maternal transcriptome during the oocyte to embryo transition. Here  we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults  yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition  transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type  suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall  our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.", null, "pubmed:33600438;pubmed:34556579", null, "WT INA R1 polyA", "GSM4724661", null, "tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB", "WT INA R1 polyA", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 92. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM", "zebrafish egg", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|developmental stage:inactive egg|strain:TLAB", "GSM4724661", "GSM4724661: WT INA R1 polyA; Danio rerio; RNA Seq", "GSM4724661", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. For rRNA depleted samples  RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific  cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM4724661", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP253077", null, null, "WT_Ooc_SQU_R1_polyA.fastq", "fastq", 1688458000.0, 16884580.0, "GSM4724661 r1", "0:100", "A:417912368;C:413739954;G:398861614;T:457809401;N:134663", 100, null, null, null, 417912368, 413739954, 398861614, 457809401, 134663, "SRX8932431", "SRS7188776", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96554, null, 0.06045, null, 0.81972, null, 0.48378, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [60104, "SRR12142045", "SRX8663215", "SRS6944340", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of lysate for FigS2", null, "zebrafish lysate biological replicate 4", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 4", "Dre 4", "cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g004_1.fastq.gz", "fastq", 509713380.0, 9994380.0, "DreSceMix g004 1.fastq.gz", "0:51", "A:251366594;C:61585710;G:62159129;T:134578953;N:22994", 51, null, null, null, 251366594, 61585710, 62159129, 134578953, 22994, "SRX8663215", "SRS6944340", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.67392, null, 0.54102, null, 0.86476, null, 0.37091, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60105, "SRR12141709", "SRX8663075", "SRS6944200", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of lysate for FigS2", null, "zebrafish lysate biological replicate 3", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 3", "Dre 3", "cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g003_1.fastq.gz", "fastq", 499717482.0, 9798382.0, "DreSceMix g003 1.fastq.gz", "0:51", "A:263221073;C:56114768;G:56547079;T:123812019;N:22543", 51, null, null, null, 263221073, 56114768, 56547079, 123812019, 22543, "SRX8663075", "SRS6944200", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.63258, null, 0.48288, null, 0.86819, null, 0.35874, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60106, "SRR12141808", "SRX8662976", "SRS6944101", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 6", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 12", "Dre 12", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g014_1.fastq.gz", "fastq", 421063599.0, 8256149.0, "DreSceMix g014 1.fastq.gz", "0:51", "A:207118237;C:53600213;G:54041718;T:106284709;N:18722", 51, null, null, null, 207118237, 53600213, 54041718, 106284709, 18722, "SRX8662976", "SRS6944101", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.47999, null, 0.19308, null, 0.85977, null, 0.46733, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60107, "SRR12141828", "SRX8662956", "SRS6944081", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 4", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 10", "Dre 10", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g012_1.fastq.gz", "fastq", 626464773.0, 12283623.0, "DreSceMix g012 1.fastq.gz", "0:51", "A:263307070;C:96744908;G:98635228;T:167749896;N:27671", 51, null, null, null, 263307070, 96744908, 98635228, 167749896, 27671, "SRX8662956", "SRS6944081", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.50608, null, 0.14369, null, 0.83422, null, 0.45691, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60108, "SRR12141839", "SRX8662945", "SRS6944070", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 3", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 9", "Dre 9", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g011_1.fastq.gz", "fastq", 436381296.0, 8556496.0, "DreSceMix g011 1.fastq.gz", "0:51", "A:205579619;C:58008903;G:59021026;T:113752218;N:19530", 51, null, null, null, 205579619, 58008903, 59021026, 113752218, 19530, "SRX8662945", "SRS6944070", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.46615, null, 0.18281, null, 0.84778, null, 0.44592, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60109, "SRR12141850", "SRX8662934", "SRS6944059", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 2", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 8", "Dre 8", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g010_1.fastq.gz", "fastq", 870727437.0, 17073087.0, "DreSceMix g010 1.fastq.gz", "0:51", "A:343772776;C:142428987;G:145570260;T:238917135;N:38279", 51, null, null, null, 343772776, 142428987, 145570260, 238917135, 38279, "SRX8662934", "SRS6944059", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.52883, null, 0.1235, null, 0.82256, null, 0.45498, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60110, "SRR12141861", "SRX8662923", "SRS6944047", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 1", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 7", "Dre 7", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g009_1.fastq.gz", "fastq", 1875928206.0, 36782906.0, "DreSceMix g009 1.fastq.gz", "0:51", "A:684015713;C:329272255;G:335557540;T:526999083;N:83615", 51, null, null, null, 684015713, 329272255, 335557540, 526999083, 83615, "SRX8662923", "SRS6944047", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.58553, null, 0.11315, null, 0.8029, null, 0.4678, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60111, "SRR12141872", "SRX8662912", "SRS6944037", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of lysate for FigS2", null, "zebrafish lysate biological replicate 6", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 6", "Dre 6", "cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g006_1.fastq.gz", "fastq", 390346044.0, 7653844.0, "DreSceMix g006 1.fastq.gz", "0:51", "A:194005234;C:46666192;G:46964771;T:102692143;N:17704", 51, null, null, null, 194005234, 46666192, 46964771, 102692143, 17704, "SRX8662912", "SRS6944037", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.69496, null, 0.57077, null, 0.86864, null, 0.35451, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60112, "SRR12141959", "SRX8662825", "SRS6943950", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of lysate for FigS2", null, "zebrafish lysate biological replicate 5", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 5", "Dre 5", "cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g005_1.fastq.gz", "fastq", 684050964.0, 13412764.0, "DreSceMix g005 1.fastq.gz", "0:51", "A:318875237;C:88359396;G:89394558;T:187391266;N:30507", 51, null, null, null, 318875237, 88359396, 89394558, 187391266, 30507, "SRX8662825", "SRS6943950", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.61659, null, 0.4142, null, 0.8393, null, 0.42049, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60113, "SRR12142001", "SRX8662783", "SRS6943908", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of purified RNA from lysate for Fig.S2", null, "zebrafish purifiedRNA biological replicate 5", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 11", "Dre 11", "cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP269853", null, null, "DreSceMix_g013_1.fastq.gz", "fastq", 998754318.0, 19583418.0, "DreSceMix g013 1.fastq.gz", "0:51", "A:402091762;C:156702863;G:160047354;T:279867921;N:44418", 51, null, null, null, 402091762, 156702863, 160047354, 279867921, 44418, "SRX8662783", "SRS6943908", "SRA1094353", "Ryukoku university|Fauculity of Agriculture", "Ryukoku university", 1, 0.52766, null, 0.13651, null, 0.81237, null, 0.45557, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2020-07-03", "Hatching", "Embryo", "Undetermined", "Embryo Imprecise"], [60114, "SRR12142002", "SRX8662782", "SRS6943907", "SRP269853", "PRJNA643885", "performance test of DeLTa Seq", "PRJNA643885", "Other", "This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq", null, null, "RNA Seq of lysate for FigS2", null, "zebrafish lysate biological replicate 2", null, "strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DeLTa Seq", "Dre 2", "Dre 2", "cDNA was synthesized with the lysate. 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