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,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,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,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,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,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,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 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,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,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,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,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,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,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,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,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,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 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,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,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,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,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 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,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,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,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,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,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,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,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,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,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,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,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,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,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,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