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93 rows where experiment.library_selection = "other", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Undetermined"

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experiment.platform 4

experiment.library_strategy 3

devstage_curation_coarse 3

tissue_curation_coarse 2

technology 2

experiment.library_layout 2

tissue_curation 1

  • Undetermined · 93 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 93 ✖

experiment.library_selection 1

  • other · 93 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9337 9337 ERR2865439 ERX2871399 ERS2871019 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 3 SAMEA5059848 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059848|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling3|common name:zebrafish|sample name:ele sibling3|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_F_CTTGTA_L004_R2_001.fastq.gz ele_sib_F_CTTGTA_L004_R1_001.fastq.gz fastq fastq 2823621200.0 14118106.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 6 0:100 1:100 A:752781583;C:663838191;G:656422705;T:750213027;N:365694 100 100     752781583 663838191 656422705 750213027 365694 ERX2871399 ERS2871019 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95595 0.95486 0.09407 0.09431 0.67529 0.67673 0.45173 0.44515 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9338 9338 ERR2865438 ERX2871398 ERS2871018 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 2 SAMEA5059847 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059847|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling2|common name:zebrafish|sample name:ele sibling2|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_D_GCCAAT_L004_R1_001.fastq.gz ele_sib_D_GCCAAT_L004_R2_001.fastq.gz fastq fastq 4217962600.0 21089813.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 5 0:100 1:100 A:1119324653;C:996982862;G:984906708;T:1116209552;N:538825 100 100     1119324653 996982862 984906708 1116209552 538825 ERX2871398 ERS2871018 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95341 0.95274 0.09215 0.09238 0.67296 0.67493 0.46185 0.4648 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9339 9339 ERR2865437 ERX2871397 ERS2871017 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     sibling 1 SAMEA5059846 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059846|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele sibling1|common name:zebrafish|sample name:ele sibling1|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_sib_B_TGACCA_L004_R1_001.fastq.gz ele_sib_B_TGACCA_L004_R2_001.fastq.gz fastq fastq 5241628000.0 26208140.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 4 0:100 1:100 A:1393802799;C:1235804455;G:1219328189;T:1392021956;N:670601 100 100     1393802799 1235804455 1219328189 1392021956 670601 ERX2871397 ERS2871017 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95296 0.95133 0.10275 0.1028 0.67018 0.67146 0.46488 0.46482 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9340 9340 ERR2865436 ERX2871396 ERS2871016 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant3 SAMEA5059845 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059845|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant3|common name:zebrafish|sample name:ele mutant3|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_E_CAGATC_L004_R1_001.fastq.gz ele_E_CAGATC_L004_R2_001.fastq.gz fastq fastq 3529752000.0 17648760.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 3 0:100 1:100 A:933354224;C:837396695;G:828677816;T:929860782;N:462483 100 100     933354224 837396695 828677816 929860782 462483 ERX2871396 ERS2871016 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.95621 0.95302 0.08584 0.08536 0.67048 0.67146 0.46615 0.46682 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9341 9341 ERR2865435 ERX2871395 ERS2871015 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant2 SAMEA5059844 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059844|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant2|common name:zebrafish|sample name:ele mutant2|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_C_ACAGTG_L004_R1_001.fastq.gz ele_C_ACAGTG_L004_R2_001.fastq.gz fastq fastq 3119723800.0 15598619.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 2 0:100 1:100 A:828335602;C:736691663;G:727853394;T:826449133;N:394008 100 100     828335602 736691663 727853394 826449133 394008 ERX2871395 ERS2871015 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.94967 0.94864 0.0992 0.09955 0.65928 0.66014 0.47042 0.46835 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9342 9342 ERR2865434 ERX2871394 ERS2871014 ERP111778 PRJEB29472 RNAseq analysis of slbp mutants in Zebrafish ena-STUDY-Department of Cell and Developmental Biology-01-11-2018-15:10:58:144-14 Other Through forward genetic screening for mutations affecting visual system development we identified prominent coloboma and cell autonomous retinal neuron differentiation lamination and retinal axon projection defects in eisspalte ele mutant zebrafish. Additional axonal deficits were present most notably at midline axon commissures. Genetic mapping and cloning of the ele mutation showed that the affected gene is slbp which encodes a conserved RNA stem loop binding protein involved in replication dependent histone mRNA metabolism. Cells throughout the central nervous system remained in the cell cycle in ele mutant embryos at stages when and locations where post mitotic cells have differentiated in wild type siblings. Indeed RNAseq analysis showed down regulation of many genes associated with neuronal differentiation. This was coincident with changes in the levels and spatial localisation of expression of various genes implicated for instance in axon guidance that likely underlie specific ele phenotypes. These results suggest that many of the cell and tissue specific phenotypes in ele mutant embryos are secondary to altered expression of modules of developmental regulatory genes that characterise or promote transitions in cell state and require the correct function of Slbp dependent histone and chromatin regulatory genes. ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 01     mutant1 SAMEA5059843 Department of Cell and Developmental Biology ENA FIRST PUBLIC:2018 11 02T17:01:55Z|ENA LAST UPDATE:2018 11 01T15:11:02Z|External Id:SAMEA5059843|INSDC center name:Department of Cell and Developmental Biology|INSDC first public:2018 11 02T17:01:55Z|INSDC last update:2018 11 01T15:11:02Z|INSDC status:public|Submitter Id:ele mutant1|common name:zebrafish|sample name:ele mutant1|scientific name:Danio rerio                 Illumina HiSeq 3000 paired end sequencing ena EXPERIMENT Department of Cell and Developmental Biology 01 11 2018 15:10:57:716 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 3000   ERP111778 Illumina HiSeq 3000 paired end sequencing ENA FIRST PUBLIC:2018 11 02|ENA LAST UPDATE:2018 11 16 ele_A_CGATGT_L004_R1_001.fastq.gz ele_A_CGATGT_L004_R2_001.fastq.gz fastq fastq 2181939600.0 10909698.0 ena RUN Department of Cell and Developmental Biology 01 11 2018 15:10:57:717 1 0:100 1:100 A:578028200;C:516249107;G:510965740;T:576417363;N:279190 100 100     578028200 516249107 510965740 576417363 279190 ERX2871394 ERS2871014 ERA1643817 Department of Cell and Developmental Biology|European Nucleotide Archive Department of Cell and Developmental Biology 2 0.94968 0.94939 0.1131 0.11293 0.66245 0.66251 0.46654 0.47475 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2018-11-01 Undetermined Embryo Undetermined Embryo Imprecise
9717 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. 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     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 2 Shield 4Ei LSU OTHER RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     10915827408.0 143629308.0 ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 2 0:76 A:3900515347;C:2409375725;G:3041696977;T:1564127293;N:112066 76       3900515347 2409375725 3041696977 1564127293 112066 ERX3854564 ERS4268611 ERA2359340 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.64398   0.40944   0.98817   0.59337   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9718 9718 ERR3842001 ERX3854563 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. 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     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 17:26:02:557 1 Shield 4Ei SSU OTHER RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     7154041880.0 94132130.0 ena RUN Computational Biology Unit 27 01 2020 17:26:02:557 1 0:76 A:2939474250;C:1489083073;G:1922522149;T:802890185;N:72223 76       2939474250 1489083073 1922522149 802890185 72223 ERX3854563 ERS4268611 ERA2359340 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.4369   0.25417   0.9867   0.60047   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9719 9719 ERR3842000 ERX3854562 ERS4268611 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. 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     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 10 Shield 4Ei OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1435748376.0 18891426.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 10 0:76 A:489056518;C:372290023;G:393663734;T:180723629;N:14472 76       489056518 372290023 393663734 180723629 14472 ERX3854562 ERS4268611 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.11942   0.03394   0.98971   0.62271   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9720 9720 ERR3841999 ERX3854561 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 9 Shield 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1168482976.0 15374776.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 9 0:76 A:516070340;C:238363428;G:268806793;T:145231087;N:11328 76       516070340 238363428 268806793 145231087 11328 ERX3854561 ERS3556006 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.22586   0.10275   0.97281   0.47683   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9721 9721 ERR3841998 ERX3854560 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 8 Shield 150NT OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1188343980.0 15636105.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 8 0:76 A:580658556;C:223116826;G:260847322;T:123709681;N:11595 76       580658556 223116826 260847322 123709681 11595 ERX3854560 ERS3556007 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.27037   0.13972   0.97392   0.39459   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9722 9722 ERR3841997 ERX3854559 ERS3556004 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 7 Shield 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1278891444.0 16827519.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 7 0:76 A:571738369;C:256385478;G:295145281;T:155610082;N:12234 76       571738369 256385478 295145281 155610082 12234 ERX3854559 ERS3556004 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.23116   0.11137   0.97932   0.45978   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9723 9723 ERR3841996 ERX3854558 ERS3556001 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 6 Sphere 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1439954368.0 18946768.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 6 0:76 A:669362698;C:280496524;G:316727778;T:173353505;N:13863 76       669362698 280496524 316727778 173353505 13863 ERX3854558 ERS3556001 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.26155   0.12068   0.96915   0.45719   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9724 9724 ERR3841995 ERX3854557 ERS3556000 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 5 Sphere 2 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1592272200.0 20950950.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 5 0:76 A:757507948;C:308394094;G:342142775;T:184211881;N:15502 76       757507948 308394094 342142775 184211881 15502 ERX3854557 ERS3556000 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.22483   0.10923   0.97646   0.49458   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9725 9725 ERR3841994 ERX3854556 ERS3555999 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 4 Sphere 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     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       529354355 299445923 318745973 184804260 13165 ERX3854556 ERS3555999 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.21197   0.0829   0.98196   0.55753   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9726 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 3 64 cell 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     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       589876602 380048242 392473318 216893826 15828 ERX3854555 ERS3555998 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.15411   0.04564   0.97883   0.55376   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9727 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 2 64 cell 4Ei OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     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       548456563 244465528 271963808 148687764 11817 ERX3854554 ERS3556003 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.21973   0.10926   0.97419   0.44348   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9728 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:405 1 64 cell 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     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       543017836 366974203 367027373 217896401 15131 ERX3854553 ERS3555997 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.2544   0.08957   0.96568   0.55681   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9729 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 33 Shield 1 F20 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       398325549 237563934 230721299 108957698 10156 ERX3511296 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.33102   0.19766   0.99918   0.12812   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9730 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 32 Shield 1 F19 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       271081669 253947035 272354427 133774815 8722 ERX3511295 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.15598   0.10707   0.99902   0.47314   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9731 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 31 Shield 1 F18 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       493273515 456544968 391677033 165002559 15193 ERX3511294 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.01562   0.0053   0.99908   0.8127   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9732 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 30 Shield 1 F17 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       471473123 333726472 302016190 152228002 12709 ERX3511293 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.18339   0.12544   0.99928   0.22368   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9733 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 29 Shield 1 F16 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       539462776 341141880 314571683 169426048 13485 ERX3511292 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.11663   0.07319   0.99939   0.25377   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9734 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 28 Shield 1 F15 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       414133320 219437277 207418049 111607418 9824 ERX3511291 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.17603   0.10972   0.99935   0.13311   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9735 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 27 Shield 1 F14 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       357710338 221475453 191231014 100526675 9148 ERX3511290 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.1248   0.06422   0.99896   0.34819   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9736 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 26 Shield 1 F13 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       434153198 223317075 198260771 125932145 9431 ERX3511289 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.44603   0.25602   0.99874   0.18074   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9737 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 25 Shield 1 F12 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       651341516 270458496 243929520 138874830 13766 ERX3511288 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.64293   0.38159   0.99886   0.07313   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9738 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 24 Shield 1 F10 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       608634206 295943144 286494431 145029697 14470 ERX3511287 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.68758   0.47517   0.99898   0.02301   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9739 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 23 Shield 1 F9 None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       658705664 297967081 295595736 182118632 15379 ERX3511286 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.74246   0.44235   0.99701   0.03112   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9740 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 22 Shield 4150NT LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     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       7153064588 5242791119 8513736630 3152547276 1068481 ERX3511285 ERS3556007 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.81267   0.27138   0.99868   0.91938   151   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9741 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 21 Shield 4150NT SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     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       4578051806 2616328922 5914185813 1878780090 651988 ERX3511284 ERS3556007 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.77096   0.5278   0.99833   0.42635   151   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9742 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 20 64 cell 4Ei 10 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       2109854905 1377083508 1616166285 824889630 60468 ERX3511283 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61525   0.45233   0.99379   0.57373   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9743 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 19 64 cell 4Ei 10 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       3901301079 2223067879 2553338016 1094797648 100158 ERX3511282 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.52103   0.25046   0.9861   0.64575   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9744 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     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                 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   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26     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       3805722011 1188715051 1382258076 353814168 216374 ERX3511281 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61922   0.37217   0.99527   0.29148   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9745 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     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                 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   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26     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       4717003484 2600725234 2586105174 712124440 346540 ERX3511280 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.30908   0.08252   0.94683   0.69548   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9746 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 16 Shield 3 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       3368038444 3190496935 3529701152 1688766119 217422 ERX3511279 ERS3556006 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.70681   0.18846   0.99332   0.71978   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9747 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 15 Shield 3 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       2990167185 1767708808 2104830363 1057568560 145036 ERX3511278 ERS3556006 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.5052   0.30841   0.99129   0.60948   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9748 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 14 Shield 2 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       4750565405 2540992255 1698817649 784832634 89061 ERX3511277 ERS3556005 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.74003   0.5616   0.99855   0.03607   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9749 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 13 Shield 2 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       3300825043 2576709678 1707115198 625376255 77126 ERX3511276 ERS3556005 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.2787   0.17583   0.99752   0.50171   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9750 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 12 Shield 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       764355184 710492003 664031460 298777374 23915 ERX3511275 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.0406   0.02417   0.99908   0.61299   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9751 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 11 Shield 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       1443205052 715251024 633421305 365333650 32345 ERX3511274 ERS3556004 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.47643   0.27944   0.99896   0.11464   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9752 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 10 Sphere 3 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       1790452280 354001675 431182140 164697730 58899 ERX3511273 ERS3556001 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.87154   0.5323   0.99793   0.02983   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9753 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 9 Sphere 3 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       3129446012 1311888416 1369035262 466745503 126999 ERX3511272 ERS3556001 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.65637   0.35975   0.9936   0.24734   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9754 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 8 Sphere 2 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     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       3113787833 1255798935 1750515950 559763997 126761 ERX3511271 ERS3556000 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.66287   0.41208   0.99602   0.17083   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9755 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 7 Sphere 2 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       7630016769 1835321568 2775223283 997916159 253985 ERX3511270 ERS3556000 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.77269   0.45994   0.99683   0.04249   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9756 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 6 Sphere 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     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       1182325939 888677953 922571204 318159754 64482 ERX3511269 ERS3555999 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.57505   0.24459   0.99582   0.43365   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9757 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 5 Sphere 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       4338227974 1233250165 1372229712 459322295 151362 ERX3511268 ERS3555999 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.765   0.44747   0.99515   0.12467   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9758 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 4 64 cell 2 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       8175036829 1396062240 1882846539 268587131 46145 ERX3511267 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.81133   0.41331   0.99823   0.03453   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9759 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3 64 cell 2 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       4813606784 2048902072 2140220088 522714000 35144 ERX3511266 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.59747   0.26784   0.996   0.21193   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9760 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2 64 cell 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     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       2633354802 2582123846 2505786164 822713754 179086 ERX3511265 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34707   0.02129   0.99797   0.62478   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9761 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1 64 cell 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   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     4628193785 2494821868 2485640988 530605907 203884 ERX3511264 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06893   0.02559   0.99766   0.90567   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9762 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2 64 cell 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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       2633354802 2582123846 2505786164 822713754 179086 ERX3437516 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34696   0.02086   0.99795   0.66261   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9763 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     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                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1 64 cell 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     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       4628193785 2494821868 2485640988 530605907 203884 ERX3437515 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06884   0.02526   0.99762   0.89856   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
10214 10214 ERR6617900 ERX6244443 ERS7291130 ERP131213 PRJEB46978 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 Other Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28   PolyA selected dRNA sequenced zebrafish 4hpf RNA Zebrafish 4hpf dRNA SAMEA9568396 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2023 12 28T01:07:30Z|ENA LAST UPDATE:2023 12 28T01:07:30Z|External Id:SAMEA9568396|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:30Z|INSDC last update:2023 12 28T01:07:30Z|INSDC status:public|Submitter Id:Zebrafish 4hpf dRNA1|common name:zebrafish|sample name:Zebrafish 4hpf dRNA1|scientific name:Danio rerio                 MinION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 dRNA Zebrafish Direct RNA Sequencing Direct RNA Sequencing   RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP131213 MinION sequencing ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 Zebrafish_4hpf_dRNA.fast5.tar.gz nanopore 772304625.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 0:860.25 A:224977035;C:165273397;G:156659356;T:225394837;N:0 860       224977035 165273397 156659356 225394837 0 ERX6244443 ERS7291130 ERA5995143 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG) 1 0.5   0.0   0.99997   1.0   962   T   long read ont ont full_length poly_a unknown bulk unknown unknown   Spain 2023-12-28 Blastula Embryo Undetermined Embryo Imprecise
11042 11042 ERR9839781 ERX9385638 ERS12199238 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep3 SAMEA110100413 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817 cDNA897892 ZFRDR3 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA897892_ZFRDR3.tar.gz nanopore 848659575.0 587586.0 ena RUN TAB 13 06 2022 16:07:52:808 818 0:1444.32 A:210205014;C:186527780;G:188214279;T:263712502;N:0 1444       210205014 186527780 188214279 263712502 0 ERX9385638 ERS12199238 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11043 11043 ERR9839780 ERX9385637 ERS12199237 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep2 SAMEA110100412 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815 cDNA123791 ZFRDR2 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA123791_ZFRDR2.tar.gz nanopore 2229275175.0 1955617.0 ena RUN TAB 13 06 2022 16:07:52:807 816 0:1139.93 A:533543922;C:498938137;G:515833119;T:680959997;N:0 1139       533543922 498938137 515833119 680959997 0 ERX9385637 ERS12199237 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11044 11044 ERR9839779 ERX9385636 ERS12199236 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep1 SAMEA110100411 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813 cDNA786327 ZFRDR1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA786327_ZFRDR1.tar.gz nanopore 1900613556.0 1660167.0 ena RUN TAB 13 06 2022 16:07:52:807 814 0:1144.83 A:473050820;C:438054520;G:425169743;T:564338473;N:0 1144       473050820 438054520 425169743 564338473 0 ERX9385636 ERS12199236 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11045 11045 ERR9839778 ERX9385635 ERS12199235 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish PolyA Selected RNA 4hpf Zebrafish pA selected SAMEA110100410 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100410|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish pA selected|common name:zebrafish|sample name:Zebrafish pA selected                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 811 cDNA852361 ZFPA4R1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA852361_ZFPA4R1.tar.gz nanopore 348224822.0 233101.0 ena RUN TAB 13 06 2022 16:07:52:807 812 0:1493.88 A:88963756;C:76104775;G:73909507;T:109246784;N:0 1493       88963756 76104775 73909507 109246784 0 ERX9385635 ERS12199235 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG) 1 0.34147   0.26829   0.99993   0.16666   1537   T   long read ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Blastula Embryo Undetermined Embryo Imprecise
33123 33123 SRR29672615 SRX25176099 SRS21866000 SRP517393 PRJNA1130538 ac4C transcriptomes of Zebrafish and Worm GSE271258 Other ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution we performed ac4C RIP seq on Zebrafish and Worm.       Zebrafish ac4C GSM8372406   tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing Zebrafish ac4C The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2 and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq the mRNA expression level was analyzed by StringTie and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format containing the expression levels and ac4C status changes for each gene. Animal organ cells   Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215 GSM8372406 GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq GSM8372406 r1 GSM8372406 1 Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502 Wuhan Seqhealth Co. Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP517393     Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz fastq fastq 816231517.0 3830403.0 GSM8372406 r1 0:102.34 1:110.76 A:199381841;C:207571478;G:205740791;T:203535549;N:1858 102 110     199381841 207571478 205740791 203535549 1858 SRX25176099 SRS21866000 SRA1914369 Fujian Medical University Fujian Medical University 2 0.60415 0.60545 0.08824 0.08794 0.78796 0.78733 0.43432 0.43842 126 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-07-01 Undetermined Undetermined Undetermined Undetermined
33886 33886 SRR30907854 SRX26311176 SRS22839346 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E2 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:9|BioSampleModel:Model organism or animal                 zebrafish 9 9 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241016_E2.R1.raw.fastq.gz L1EFA241016_E2.R2.raw.fastq.gz fastq fastq 8244899282.0 27300991.0 L1EFA241016 E2.R1.raw.fastq.gz 0:151 1:151 A:2186915781;C:1920264424;G:1996130250;T:2141502974;N:85853 151 151     2186915781 1920264424 1996130250 2141502974 85853 SRX26311176 SRS22839346 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33887 33887 SRR30907855 SRX26311175 SRS22839344 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E1 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:7|BioSampleModel:Model organism or animal                 zebrafish 7 7 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241015_E1.R1.raw.fastq.gz L1EFA241015_E1.R2.raw.fastq.gz fastq fastq 7083661566.0 23455833.0 L1EFA241015 E1.R1.raw.fastq.gz 0:151 1:151 A:1848193884;C:1679679234;G:1751186922;T:1804529897;N:71629 151 151     1848193884 1679679234 1751186922 1804529897 71629 SRX26311175 SRS22839344 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33888 33888 SRR30907856 SRX26311174 SRS22839345 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A3 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:5|BioSampleModel:Model organism or animal                 zebrafish 5 5 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241014_A3.R1.raw.fastq.gz L1EFA241014_A3.R2.raw.fastq.gz fastq fastq 7926170898.0 26245599.0 L1EFA241014 A3.R1.raw.fastq.gz 0:151 1:151 A:2128209130;C:1819597773;G:1900902610;T:2077378388;N:82997 151 151     2128209130 1819597773 1900902610 2077378388 82997 SRX26311174 SRS22839345 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33889 33889 SRR30907857 SRX26311173 SRS22839343 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A2 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:3|BioSampleModel:Model organism or animal                 zebrafish 3 3 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241013_A2.R1.raw.fastq.gz L1EFA241013_A2.R2.raw.fastq.gz fastq fastq 7889851774.0 26125337.0 L1EFA241013 A2.R1.raw.fastq.gz 0:151 1:151 A:2121620438;C:1812268472;G:1879664190;T:2076216345;N:82329 151 151     2121620438 1812268472 1879664190 2076216345 82329 SRX26311173 SRS22839343 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33890 33890 SRR30907858 SRX26311172 SRS22839342 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish E3 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:11|BioSampleModel:Model organism or animal                 zebrafish 11 11 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241017_E3.R1.raw.fastq.gz L1EFA241017_E3.R2.raw.fastq.gz fastq fastq 7824546992.0 25909096.0 L1EFA241017 E3.R1.raw.fastq.gz 0:151 1:151 A:2082463940;C:1810596613;G:1891675714;T:2039730477;N:80248 151 151     2082463940 1810596613 1891675714 2039730477 80248 SRX26311172 SRS22839342 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
33891 33891 SRR30907859 SRX26311171 SRS22839341 SRP537088 PRJNA1167252 Eukaryotic transcriptome sequencing of zebrafish PRJNA1167252 Other To study the effects of TDCPP reports on protein expression and RNA transcription in zebrafish       zebrafish A1 R1   strain:zebrafish|isolate:missing|breed:AB|cultivar:missing|ecotype:missing|age:48hpf|dev stage:48hpf|collection date:2023 11 30|geo loc name:missing|sex:missing|tissue:missing|tmp:1|BioSampleModel:Model organism or animal                 zebrafish 1 1 Effects of TDCPP exposure on transcription in zebrafish     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina MiSeq   SRP537088     L1EFA241012_A1.R1.raw.fastq.gz L1EFA241012_A1.R2.raw.fastq.gz fastq fastq 8017250474.0 26547187.0 L1EFA241012 A1.R1.raw.fastq.gz 0:151 1:151 A:2139416119;C:1853218216;G:1930287523;T:2094246996;N:81620 151 151     2139416119 1853218216 1930287523 2094246996 81620 SRX26311171 SRS22839341 SRA1987398 Beijing Normal University|College of Water Sciences Beijing Normal University                       B B biological fallback assumption illumina miseq unknown other unknown bulk unknown unknown   China 2024-10-08 Hatching Embryo Undetermined Embryo Imprecise
50535 50535 SRR8134458 SRX4955494 SRS3996631 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 3 H24 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_3_R1.fastq H24_3_R2.fastq fastq fastq 1303220750.0 5212883.0 H24 3 R1.fastq 0:125 1:125 A:353042196;C:298548859;G:299882991;T:351742904;N:3800 125 125     353042196 298548859 299882991 351742904 3800 SRX4955494 SRS3996631 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.95284 0.94903 0.03485 0.03522 0.8606 0.86168 0.49556 0.49795 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50536 50536 SRR8134459 SRX4955493 SRS3996630 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 1 H24 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_1_R1.fastq H24_1_R2.fastq fastq fastq 1040367750.0 4161471.0 H24 1 R1.fastq 0:125 1:125 A:285190807;C:235796611;G:237165817;T:282211556;N:2959 125 125     285190807 235796611 237165817 282211556 2959 SRX4955493 SRS3996630 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94648 0.94488 0.0507 0.05253 0.87353 0.87513 0.52936 0.52764 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50537 50537 SRR8134460 SRX4955492 SRS3996629 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 2 H24 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_2_R1.fastq H24_2_R2.fastq fastq fastq 1003243000.0 4012972.0 H24 2 R1.fastq 0:125 1:125 A:275192369;C:227024454;G:228346661;T:272676506;N:3010 125 125     275192369 227024454 228346661 272676506 3010 SRX4955492 SRS3996629 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94467 0.94348 0.06361 0.06541 0.8423 0.84478 0.51257 0.51745 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50538 50538 SRR8134461 SRX4955491 SRS3996628 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 2 H11 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_2_R1.fastq H11_2_R2.fastq fastq fastq 1034277500.0 4137110.0 H11 2 R1.fastq 0:125 1:125 A:286346530;C:232910512;G:234755237;T:280262966;N:2255 125 125     286346530 232910512 234755237 280262966 2255 SRX4955491 SRS3996628 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94693 0.94598 0.03067 0.03082 0.8562 0.85774 0.51961 0.51451 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50539 50539 SRR8134462 SRX4955490 SRS3996627 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 3 H11 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_3_R1.fastq H11_3_R2.fastq fastq fastq 1084328250.0 4337313.0 H11 3 R1.fastq 0:125 1:125 A:296459005;C:246835042;G:248291057;T:292740098;N:3048 125 125     296459005 246835042 248291057 292740098 3048 SRX4955490 SRS3996627 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.95199 0.95021 0.02101 0.02158 0.85914 0.86058 0.51593 0.41299 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50540 50540 SRR8134463 SRX4955489 SRS3996626 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 3 H6 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_3_R1.fastq H6_3_R2.fastq fastq fastq 989016500.0 3956066.0 H6 3 R1.fastq 0:125 1:125 A:270941686;C:224568911;G:226264637;T:267238750;N:2516 125 125     270941686 224568911 226264637 267238750 2516 SRX4955489 SRS3996626 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94889 0.94713 0.02757 0.02789 0.84415 0.84571 0.52218 0.52291 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise
50541 50541 SRR8134464 SRX4955488 SRS3996623 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 1 H11 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_1_R1.fastq H11_1_R2.fastq fastq fastq 707998500.0 2831994.0 H11 1 R1.fastq 0:125 1:125 A:194434087;C:160870744;G:162119289;T:190572787;N:1593 125 125     194434087 160870744 162119289 190572787 1593 SRX4955488 SRS3996623 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94561 0.94128 0.03328 0.03394 0.8589 0.86062 0.48582 0.48548 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50542 50542 SRR8134465 SRX4955487 SRS3996624 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 1 H6 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_1_R1.fastq H6_1_R2.fastq fastq fastq 759809500.0 3039238.0 H6 1 R1.fastq 0:125 1:125 A:211499426;C:170044275;G:171920878;T:206342561;N:2360 125 125     211499426 170044275 171920878 206342561 2360 SRX4955487 SRS3996624 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94965 0.94791 0.04309 0.04276 0.83485 0.83676 0.5519 0.56156 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise
50543 50543 SRR8134466 SRX4955486 SRS3996625 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 2 H6 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_2_R1.fastq H6_2_R2.fastq fastq fastq 858125000.0 3432500.0 H6 2 R1.fastq 0:125 1:125 A:236752508;C:193146437;G:194455657;T:233768197;N:2201 125 125     236752508 193146437 194455657 233768197 2201 SRX4955486 SRS3996625 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94359 0.93966 0.04047 0.03943 0.83924 0.84396 0.54153 0.54602 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise
52210 52210 SRR9021058 SRX5799154 SRS4730324 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 1   replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 1 20190506 1 WT 1 20190506 1 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT1.1.fq fastq 1094498950.0 21889979.0 WT1.1.fq 0:50 A:291195764;C:255539280;G:262638316;T:284737693;N:387897 50       291195764 255539280 262638316 284737693 387897 SRX5799154 SRS4730324 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94195   0.09713   0.66689   0.47749   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52211 52211 SRR9021059 SRX5799153 SRS4730323 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 2   replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 2 20190506 2 WT 2 20190506 2 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT2.1.fq fastq 1095133200.0 21902664.0 WT2.1.fq 0:50 A:290594757;C:255644044;G:259681140;T:288014102;N:1199157 50       290594757 255644044 259681140 288014102 1199157 SRX5799153 SRS4730323 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.93368   0.09166   0.67085   0.46523   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52212 52212 SRR9021060 SRX5799152 SRS4730322 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         WT 3   replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome WT 3 20190506 3 WT 3 20190506 3 RNA seq of WT Diano rerio     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py WT3.1.fq fastq 1096083900.0 21921678.0 WT3.1.fq 0:50 A:290332094;C:256993500;G:263043956;T:285349722;N:364628 50       290332094 256993500 263043956 285349722 364628 SRX5799152 SRS4730322 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94147   0.10157   0.66135   0.47301   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52213 52213 SRR9021061 SRX5799151 SRS4730320 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 1   replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 1 20190506 1 gcgr 1 20190506 1 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr1.1.fq fastq 1096307200.0 21926144.0 gcgr1.1.fq 0:50 A:288839446;C:258297625;G:264630675;T:284199738;N:339716 50       288839446 258297625 264630675 284199738 339716 SRX5799151 SRS4730320 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94131   0.09307   0.67574   0.46993   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52214 52214 SRR9021062 SRX5799150 SRS4730321 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 2   replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 2 20190506 2 gcgr 2 20190506 2 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr2.1.fq fastq 1094410100.0 21888202.0 gcgr2.1.fq 0:50 A:290062779;C:256358687;G:264488431;T:282812212;N:687991 50       290062779 256358687 264488431 282812212 687991 SRX5799150 SRS4730321 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94074   0.09337   0.67633   0.46861   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
52215 52215 SRR9021063 SRX5799149 SRS4730319 SRP195685 PRJNA541367 Global transcriptomic analysis of zebrafish glucagon receptor mutant PRJNA541367 Other We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study.         gcgr 3   replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal                 Diano rerio transcriptome gcgr 3 20190506 3 gcgr 3 20190506 3 RNA seq of Diano rerio with gcgr mutant     RNA-Seq TRANSCRIPTOMIC other SINGLE BGISEQ BGISEQ-500   SRP195685   loader:fastq load.py gcgr3.1.fq fastq 1094284800.0 21885696.0 gcgr3.1.fq 0:50 A:289313514;C:257096636;G:264011408;T:283143600;N:719642 50       289313514 257096636 264011408 283143600 719642 SRX5799149 SRS4730319 SRA883435 Xiamen University|School of Pharmaceutical Sciences Xiamen University 1 0.94222   0.09557   0.67521   0.46664   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-18 Larval Larval Undetermined Undetermined
59497 59497 SRR11924327 SRX8469999 SRS6770650 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA oblong 2 GSM4591066   source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA oblong 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. oblong   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591066 GSM4591066: small RNA oblong 2; Danio rerio; OTHER GSM4591066   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591066 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_oblong_stage_2.fastq fastq 131762340.0 2740821.0 GSM4591066 r1 0:48.07 A:36963883;C:35740715;G:33446415;T:25611327;N:0 48       36963883 35740715 33446415 25611327 0 SRX8469999 SRS6770650 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.5346   0.11052   0.8967   0.64134   72   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
59498 59498 SRR11924326 SRX8469998 SRS6770649 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA oblong 1 GSM4591065   source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA oblong 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. oblong   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591065 GSM4591065: small RNA oblong 1; Danio rerio; OTHER GSM4591065   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591065 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_oblong_stage_1.fastq fastq 90701340.0 2141489.0 GSM4591065 r1 0:42.35 A:25203959;C:24291162;G:23143516;T:18062703;N:0 42       25203959 24291162 23143516 18062703 0 SRX8469998 SRS6770649 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.48132   0.15952   0.8756   0.56134   29   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
59499 59499 SRR11924325 SRX8469997 SRS6770648 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA 32 cell GSM4591064   source name:32 cell stage|tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA 32 cell Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 32 cell stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591064 GSM4591064: small RNA 32 cell; Danio rerio; OTHER GSM4591064   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591064 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_32_cell_stage.fastq fastq 275040056.0 6091077.0 GSM4591064 r1 0:45.15 A:69136092;C:69806677;G:72527986;T:63569301;N:0 45       69136092 69806677 72527986 63569301 0 SRX8469997 SRS6770648 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.67676   0.30881   0.86636   0.63482   22   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Cleavage Embryo Undetermined Embryo Imprecise
59500 59500 SRR11924324 SRX8469996 SRS6770647 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA 15E GSM4591063   source name:zfs:0000015|tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA 15E Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. zfs:0000015   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591063 GSM4591063: small RNA 15E; Danio rerio; OTHER GSM4591063   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591063 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_15E_stage.fastq fastq 264453879.0 5777826.0 GSM4591063 r1 0:45.77 A:63859672;C:67381369;G:71681258;T:61531580;N:0 45       63859672 67381369 71681258 61531580 0 SRX8469996 SRS6770647 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.60375   0.23463   0.87606   0.58681   40   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
59503 59503 SRR11924320 SRX8469993 SRS6770644 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   PM 3 GSM4591060   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 3 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. protruding mouth stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591060 GSM4591060: PM 3; Danio rerio; OTHER GSM4591060   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591060 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_3.bam bam bam 215125332.0 6403488.0 GSM4591060 r1 0:33.60 A:50202267;C:65116674;G:52637331;T:47169060;N:0 33       50202267 65116674 52637331 47169060 0 SRX8469993 SRS6770644 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.73594   0.21617   0.86251   0.68892   42   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined
59504 59504 SRR11924318 SRX8469992 SRS6770643 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   PM 2 GSM4591059   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. protruding mouth stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591059 GSM4591059: PM 2; Danio rerio; OTHER GSM4591059   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591059 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_2.bam bam bam 426315355.0 12915702.0 GSM4591059 r1 0:33.01 A:92276988;C:141702085;G:104175159;T:88161123;N:0 33       92276988 141702085 104175159 88161123 0 SRX8469992 SRS6770643 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.76385   0.1921   0.87207   0.71495   40   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined
59505 59505 SRR11924317 SRX8469990 SRS6770641 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   PM 1 GSM4591058   source name:protruding mouth stage|tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA PM 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. protruding mouth stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:protruding mouth stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591058 GSM4591058: PM 1; Danio rerio; OTHER GSM4591058   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591058 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate GSE151797_Reference_sequence.fa PM_1.bam bam bam 130388595.0 5124384.0 GSM4591058 r1 0:25.44 A:27290253;C:42592303;G:31075292;T:29430747;N:0 25       27290253 42592303 31075292 29430747 0 SRX8469990 SRS6770641 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.78884   0.23004   0.85113   0.67571   38   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Larval Larval Undetermined Undetermined
59506 59506 SRR11924315 SRX8469989 SRS6770640 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   12 somite 3 GSM4591057   source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA 12 somite 3 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 12 somite stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591057 GSM4591057: 12 somite 3; Danio rerio; OTHER GSM4591057   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591057 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 12_somite_3.bam GSE151797_Reference_sequence.fa bam bam 105146264.0 3189309.0 GSM4591057 r1 0:32.97 A:24684898;C:33906144;G:26247070;T:20308152;N:0 32       24684898 33906144 26247070 20308152 0 SRX8469989 SRS6770640 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.83304   0.22816   0.88325   0.69597   43   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Segmentation Embryo Undetermined Embryo Imprecise
59507 59507 SRR11924314 SRX8469988 SRS6770639 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   12 somite 2 GSM4591056   source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA 12 somite 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 12 somite stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591056 GSM4591056: 12 somite 2; Danio rerio; OTHER GSM4591056   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591056 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 12_somite_2.bam GSE151797_Reference_sequence.fa bam bam 255844263.0 7971494.0 GSM4591056 r1 0:32.09 A:53703561;C:85057062;G:64342817;T:52740823;N:0 32       53703561 85057062 64342817 52740823 0 SRX8469988 SRS6770639 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.79601   0.23342   0.90281   0.75464   40   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Segmentation Embryo Undetermined Embryo Imprecise
59508 59508 SRR11924312 SRX8469987 SRS6770638 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   12 somite 1 GSM4591055   source name:12 somite stage|tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA 12 somite 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 12 somite stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:12 somite stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591055 GSM4591055: 12 somite 1; Danio rerio; OTHER GSM4591055   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591055 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 12_somite_1.bam GSE151797_Reference_sequence.fa bam bam 254000103.0 7990851.0 GSM4591055 r1 0:31.79 A:52359510;C:82090735;G:62850013;T:56699845;N:0 31       52359510 82090735 62850013 56699845 0 SRX8469987 SRS6770638 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.69554   0.21063   0.88284   0.72326   43   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Segmentation Embryo Undetermined Embryo Imprecise
59509 59509 SRR11924311 SRX8469986 SRS6770637 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   32 cell 3 GSM4591054   source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA 32 cell 3 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 32 cell stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591054 GSM4591054: 32 cell 3; Danio rerio; OTHER GSM4591054   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591054 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 32_cell_3.bam GSE151797_Reference_sequence.fa bam bam 306452866.0 9472058.0 GSM4591054 r1 0:32.35 A:62923439;C:99486553;G:78734118;T:65308756;N:0 32       62923439 99486553 78734118 65308756 0 SRX8469986 SRS6770637 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.69616   0.21356   0.91885   0.77399   44   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Cleavage Embryo Undetermined Embryo Imprecise
59510 59510 SRR11924310 SRX8469985 SRS6770636 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   32 cell 2 GSM4591053   source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA 32 cell 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 32 cell stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591053 GSM4591053: 32 cell 2; Danio rerio; OTHER GSM4591053   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591053 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 32_cell_2.bam GSE151797_Reference_sequence.fa bam bam 231900531.0 6985149.0 GSM4591053 r1 0:33.20 A:46033127;C:77390842;G:61355372;T:47121190;N:0 33       46033127 77390842 61355372 47121190 0 SRX8469985 SRS6770636 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.83429   0.25864   0.9137   0.78928   39   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Cleavage Embryo Undetermined Embryo Imprecise
59511 59511 SRR11924308 SRX8469984 SRS6770635 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   32 cell 1 GSM4591052   source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA 32 cell 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. 32 cell stage   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description   tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA GSM4591052 GSM4591052: 32 cell 1; Danio rerio; OTHER GSM4591052   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U Christensen Dalsgaard M Krogh N Sabarinathan R Gorodkin J Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description GEO Accession:GSM4591052 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent Proton   SRP265951   intentional duplicate 32_cell_1.bam GSE151797_Reference_sequence.fa bam bam 252107732.0 7470443.0 GSM4591052 r1 0:33.75 A:53056857;C:79089015;G:65131744;T:54830116;N:0 33       53056857 79089015 65131744 54830116 0 SRX8469984 SRS6770635 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.78874   0.25062   0.89645   0.73533   48   B   usable mapping rate ion_torrent ion_torrent 5prime small_rna unknown bulk unknown unknown   Denmark 2020-06-04 Cleavage Embryo Undetermined Embryo Imprecise

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;