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
0,DRR314108,DRX303511,DRS233566,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample3,SAMD00399013,,sample name:rna rw337 48hpf WT rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399013,DRX303511,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399013,,,,23076492885.0,76679376.0,DRR314108,0:150.51 1:150.44,A:6146969533;C:5373690527;G:5458576301;T:6095818756;N:1437768,150,150,,,6146969533,5373690527,5458576301,6095818756,1437768,DRX303511,DRS233566,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94223,0.94614,0.10721,0.10288,0.68745,0.68621,0.4728,0.47157,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
1,DRR314107,DRX303510,DRS233565,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample2,SAMD00399012,,sample name:rna rw337 48hpf WT rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399012,DRX303510,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399012,,,,26091623771.0,86694066.0,DRR314107,0:150.51 1:150.45,A:6955374552;C:6050013285;G:6169385096;T:6915281392;N:1569446,150,150,,,6955374552,6050013285,6169385096,6915281392,1569446,DRX303510,DRS233565,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94028,0.94277,0.11038,0.10462,0.68288,0.68134,0.46992,0.47227,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
2,DRR314106,DRX303509,DRS233564,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of wild type sibling sample1,SAMD00399011,,sample name:rna rw337 48hpf WT rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399011,DRX303509,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399011,,,,23833525756.0,79191795.0,DRR314106,0:150.51 1:150.44,A:6324521565;C:5556755459;G:5694025045;T:6256748423;N:1475264,150,150,,,6324521565,5556755459,5694025045,6256748423,1475264,DRX303509,DRS233564,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.94723,0.94975,0.09521,0.09114,0.6776,0.67819,0.46045,0.46153,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
3,DRR314105,DRX303508,DRS233563,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample3,SAMD00399010,,sample name:rna rw337 48hpf Mutant rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399010,DRX303508,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399010,,,,27688386114.0,92009317.0,DRR314105,0:150.49 1:150.44,A:7681451080;C:6071566134;G:6242782106;T:7690830655;N:1756139,150,150,,,7681451080,6071566134,6242782106,7690830655,1756139,DRX303508,DRS233563,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.91038,0.91556,0.17971,0.16967,0.67718,0.67716,0.47042,0.46425,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
4,DRR314104,DRX303507,DRS233562,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample2,SAMD00399009,,sample name:rna rw337 48hpf Mutant rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399009,DRX303507,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399009,,,,22970994572.0,76322352.0,DRR314104,0:150.52 1:150.46,A:6142535654;C:5310453740;G:5430124468;T:6086516676;N:1364034,150,150,,,6142535654,5310453740,5430124468,6086516676,1364034,DRX303507,DRS233562,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.93707,0.94063,0.12175,0.11613,0.67825,0.67649,0.46485,0.46905,147,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
5,DRR314103,DRX303506,DRS233561,DRP008373,PRJDB12134,Comparison of expression profile between banp mutant and wildtype sibling.,DRP008373,Other,To characterize the physiological function of Banp the expression profile of banp mutant and wild type sibling was obtained by ATAC sequencing and RNA sequencing. All data were obtained using embryo heads at 48 hpf.,,,,RNA seq of banp mutant sample1,SAMD00399008,,sample name:rna rw337 48hpf Mutant rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00399008,DRX303506,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008373,Illumina NovaSeq 6000 paired end sequencing of SAMD00399008,,,,23637901630.0,78541449.0,DRR314103,0:150.51 1:150.45,A:6359178134;C:5420730443;G:5530700546;T:6325864263;N:1428244,150,150,,,6359178134,5420730443,5530700546,6325864263,1428244,DRX303506,DRS233561,DRA012572,OIST|Developmental Neurobiology Unit,Okinawa Institute of Science and Technology,2,0.9308,0.93545,0.13172,0.12462,0.68219,0.6814,0.46842,0.46984,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2022-04-01,Hatching,Embryo,Undetermined,Embryo Imprecise
6,DRR315802,DRX305194,DRS231989,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample4,SAMD00400823,,sample name:rw147 2.5dpf wildtype rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,DRX305194,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400823,,,,10262353995.0,34151547.0,DRR315802,0:150.27 1:150.22,A:2735078560;C:2386126821;G:2433638250;T:2707202814;N:307550,150,150,,,2735078560,2386126821,2433638250,2707202814,307550,DRX305194,DRS231989,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95231,0.95295,0.09229,0.08773,0.71819,0.72107,0.46746,0.46617,151,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
7,DRR315801,DRX305193,DRS231988,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample3,SAMD00400822,,sample name:rw147 2.5dpf wildtype rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,DRX305193,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400822,,,,11516368634.0,38355888.0,DRR315801,0:150.15 1:150.10,A:3080341643;C:2678048339;G:2713051368;T:3044449330;N:477954,150,150,,,3080341643,2678048339,2713051368,3044449330,477954,DRX305193,DRS231988,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95353,0.95634,0.08909,0.08533,0.71374,0.71252,0.45986,0.46059,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
8,DRR315800,DRX305192,DRS231987,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample2,SAMD00400821,,sample name:rw147 2.5dpf wildtype rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,DRX305192,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400821,,,,8814057148.0,29367513.0,DRR315800,0:150.09 1:150.04,A:2350403211;C:2054073465;G:2083044327;T:2326181188;N:354957,150,150,,,2350403211,2054073465,2083044327,2326181188,354957,DRX305192,DRS231987,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95287,0.95643,0.0891,0.08586,0.70309,0.70252,0.46384,0.46281,151,149,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
9,DRR315799,DRX305191,DRS231986,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,wildtype sibling sample1,SAMD00400820,,sample name:rw147 2.5dpf wildtype rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,DRX305191,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400820,,,,10491955578.0,34900682.0,DRR315799,0:150.34 1:150.28,A:2796521111;C:2446218287;G:2483414564;T:2765477785;N:323831,150,150,,,2796521111,2446218287,2483414564,2765477785,323831,DRX305191,DRS231986,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9539,0.95646,0.08185,0.07808,0.70025,0.70013,0.44713,0.44987,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
10,DRR315798,DRX305190,DRS231985,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample4,SAMD00400819,,sample name:rw147 2.5dpf Mutant rep 4|biological replicate:4,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,DRX305190,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400819,,,,9197802250.0,30604326.0,DRR315798,0:150.30 1:150.24,A:2468967963;C:2130949980;G:2158692262;T:2438931017;N:261028,150,150,,,2468967963,2130949980,2158692262,2438931017,261028,DRX305190,DRS231985,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95159,0.95439,0.10146,0.09758,0.71995,0.71983,0.46519,0.46797,150,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
11,DRR315797,DRX305189,DRS231984,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample3,SAMD00400818,,sample name:rw147 2.5dpf Mutant rep 3|biological replicate:3,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,DRX305189,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400818,,,,10498982078.0,34931731.0,DRR315797,0:150.31 1:150.25,A:2804535103;C:2445295179;G:2478768789;T:2770066062;N:316945,150,150,,,2804535103,2445295179,2478768789,2770066062,316945,DRX305189,DRS231984,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95448,0.95652,0.0939,0.0887,0.71796,0.71847,0.46335,0.46615,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
12,DRR315796,DRX305188,DRS231983,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample2,SAMD00400817,,sample name:rw147 2.5dpf Mutant rep 2|biological replicate:2,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,DRX305188,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400817,,,,9850145990.0,32782079.0,DRR315796,0:150.26 1:150.21,A:2636205537;C:2286508705;G:2319481100;T:2607600624;N:350024,150,150,,,2636205537,2286508705,2319481100,2607600624,350024,DRX305188,DRS231983,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.95193,0.95472,0.09722,0.09375,0.7138,0.71299,0.45542,0.45994,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
13,DRR315795,DRX305187,DRS231982,DRP008318,PRJDB12206,Transcriptome analysis of strip1 mutant and wildtype zebrafish eyes,DRP008318,Transcriptome Analysis,"Strip1 plays essential roles in the developing zebrafish retinal neural circuit. To identify the underlying molecular mechanisms at the transcriptomic level transcriptome of strip1 mutant ""rw147"" eye cups at 2.5 dpf was compared to that of wild type siblings using bulk RNA sequencing analysis.",,,,strip1 mutant sample1,SAMD00400816,,sample name:rw147 2.5dpf Mutant rep 1|biological replicate:1,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,DRX305187,1,1,1,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,1510Application ReadForward11Application ReadReverse76,DRP008318,Illumina NovaSeq 6000 paired end sequencing of SAMD00400816,,,,9542039835.0,31780260.0,DRR315795,0:150.15 1:150.10,A:2543384204;C:2224374632;G:2258183435;T:2515655339;N:442225,150,150,,,2543384204,2224374632,2258183435,2515655339,442225,DRX305187,DRS231982,DRA012640,OIST|Developmental Neurobiology Unit,Developmental Neurobiology Unit,2,0.9528,0.95591,0.08656,0.0828,0.70352,0.70331,0.45316,0.44914,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,Unknown,2022-03-16,Hatching,Embryo,Undetermined,Embryo Imprecise
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
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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
9919,ERR5167510,ERX4972431,ERS5593364,ERP122761,PRJEB39265,RNA dynamics during zebrafish development,ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183,Other,RNA dynamics during early zebrafish development,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,cDNA WT 2hpf rep1,JD T20 PDPN191089,,ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,,,,,PromethION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,OXFORD_NANOPORE,PromethION,,ERP122761,PromethION sequencing,ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05,,,,,ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1,,,,,,,,,,,,ERX4972431,,ERA3319053,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,unknown,poly_a,unknown,bulk,unknown,unknown,,Spain,2022-07-05,Cleavage,Embryo,Undetermined,Embryo Imprecise
10212,ERR6511331,ERX6138167,ERS7264190,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,,Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA,Zebrafish PolyA 4 hpf,SAMEA9541420,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,cDNA8523612,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_polya_4hpf.tar.gz,nanopore,330562220.0,233101.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5,0:1418.11,A:86572446;C:74232962;G:69203462;T:100553350;N:0,1418,,,,86572446,74232962,69203462,100553350,0,ERX6138167,ERS7264190,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.0,,0.0,,1.0,,,,1536,,T,,long read,ont,ont,full_length,poly_a,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Blastula,Embryo,Undetermined,Embryo Imprecise
10213,ERR6511329,ERX6138165,ERS7264188,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,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep1,SAMEA9541418,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541418|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep1|common name:zebrafish|sample name:Zebrafish Ribodep Rep1|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,cDNA786327,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep1.tar.gz,nanopore,1745399583.0,1644167.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 3,0:1061.57,A:449704009;C:421915878;G:378879857;T:494899839;N:0,1061,,,,449704009,421915878,378879857,494899839,0,ERX6138165,ERS7264188,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),1,0.01112,,0.0,,0.99997,,1.0,,546,,T,,long read,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,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
10215,ERR6511330,ERX6138166,ERS7264189,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,,Zebrafish Nano3P seq of Ribodepleted sample biological replicate 1 including 2 hpf 4 hpf 6 hpf RNAs,Zebrafish Ribodep Rep2,SAMEA9541419,CENTER FOR GENOMIC REGULATION (CRG),ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541419|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish Ribodep Rep2|common name:zebrafish|sample name:Zebrafish Ribodep Rep2|scientific name:Danio rerio,,,,,,,,,MinION sequencing,ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,cDNA123791,Nano3P seq,Nano3P seq,,OTHER,TRANSCRIPTOMIC,unspecified,SINGLE,OXFORD_NANOPORE,MinION,,ERP131213,MinION sequencing,ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28,zebrafish_ribodep_rep2.tar.gz,nanopore,2038398139.0,1955617.0,ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 4,0:1042.33,A:518369802;C:477535545;G:441294056;T:601198736;N:0,1042,,,,518369802,477535545,441294056,601198736,0,ERX6138166,ERS7264189,ERA5757997,CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive,CENTER FOR GENOMIC REGULATION (CRG),,,,,,,,,,,,,,,ont,ont,full_length,rrna_depletion,unknown,bulk,unknown,unknown,,Spain,2023-12-28,Multi-stage,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
14875,ERR12071836,ERX11454461,ERS16387703,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E115 1,SAMEA114399011,University of East Anglia,ENA FIRST PUBLIC:2023 10 06T08:31:44Z|ENA LAST UPDATE:2023 10 06T08:31:44Z|External Id:SAMEA114399011|INSDC center name:University of East Anglia|INSDC first public:2023 10 06T08:31:44Z|INSDC last update:2023 10 06T08:31:44Z|INSDC status:public|Submitter Id:115 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66715,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 10 06|ENA LAST UPDATE:2023 10 06,115-1_S69_L006_R1_001.fastq.gz 115-1_S69_L006_R2_001.fastq.gz,fastq fastq,12813280704.0,50846352.0,ena RUN TAB 21 09 2023 13:32:15:295 66716,0:126 1:126,A:2451295493;C:3891843753;G:4001866488;T:2448421880;N:19853090,126,126,,,2451295493,3891843753,4001866488,2448421880,19853090,ERX11454461,ERS16387703,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.89907,0.8514,0.17845,0.173,0.80369,0.81085,0.83252,0.83449,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14876,ERR12071855,ERX11454480,ERS16387722,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E83 5,SAMEA114399030,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:83 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:300 66753,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,83-5_S40_L008_R1_001.fastq.gz 83-5_S40_L008_R2_001.fastq.gz,fastq fastq,13683493656.0,54299578.0,ena RUN TAB 21 09 2023 13:32:15:300 66754,0:126 1:126,A:2772843483;C:4073415925;G:4192640412;T:2641952920;N:2640916,126,126,,,2772843483,4073415925,4192640412,2641952920,2640916,ERX11454480,ERS16387722,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.92452,0.92427,0.15846,0.16251,0.7777,0.77666,0.78362,0.77515,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14877,ERR12071854,ERX11454479,ERS16387721,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E83 4,SAMEA114399029,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:83 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66751,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,83-4_S8_L002_R1_001.fastq.gz 83-4_S8_L002_R2_001.fastq.gz,fastq fastq,10045714644.0,39863947.0,ena RUN TAB 21 09 2023 13:32:15:300 66752,0:126 1:126,A:2037388456;C:2963530056;G:3069663461;T:1972981871;N:2150800,126,126,,,2037388456,2963530056,3069663461,1972981871,2150800,ERX11454479,ERS16387721,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.91872,0.91762,0.16049,0.16307,0.76516,0.76644,0.77023,0.77199,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14878,ERR12071853,ERX11454478,ERS16387720,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E83 3,SAMEA114399028,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:83 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66749,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,83-3_S12_L003_R1_001.fastq.gz 83-3_S12_L003_R2_001.fastq.gz,fastq fastq,17333567748.0,68783999.0,ena RUN TAB 21 09 2023 13:32:15:299 66750,0:126 1:126,A:3399006637;C:5245167754;G:5416988818;T:3269621086;N:2783453,126,126,,,3399006637,5245167754,5416988818,3269621086,2783453,ERX11454478,ERS16387720,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.93044,0.93099,0.14459,0.1479,0.77287,0.774,0.78248,0.78348,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14879,ERR12071852,ERX11454477,ERS16387719,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E83 1,SAMEA114399027,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:83 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:83 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66747,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,83-1_S4_L001_R1_001.fastq.gz 83-1_S4_L001_R2_001.fastq.gz,fastq fastq,14977164132.0,59433191.0,ena RUN TAB 21 09 2023 13:32:15:299 66748,0:126 1:126,A:3115980365;C:4357431505;G:4531888641;T:2968758582;N:3105039,126,126,,,3115980365,4357431505,4531888641,2968758582,3105039,ERX11454477,ERS16387719,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.89622,0.89549,0.15698,0.16074,0.76558,0.76779,0.70301,0.73129,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14880,ERR12071851,ERX11454476,ERS16387718,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E82 5,SAMEA114399026,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:82 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:299 66745,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,82-5_S3_L001_R1_001.fastq.gz 82-5_S3_L001_R2_001.fastq.gz,fastq fastq,14575744764.0,57840257.0,ena RUN TAB 21 09 2023 13:32:15:299 66746,0:126 1:126,A:3079286238;C:4161280385;G:4315514217;T:3016549159;N:3114765,126,126,,,3079286238,4161280385,4315514217,3016549159,3114765,ERX11454476,ERS16387718,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.82553,0.82489,0.15941,0.16124,0.77337,0.77518,0.73773,0.75718,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14881,ERR12071850,ERX11454475,ERS16387717,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E82 3,SAMEA114399025,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:82 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66743,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,82-3_S11_L003_R1_001.fastq.gz 82-3_S11_L003_R2_001.fastq.gz,fastq fastq,15753924144.0,62515572.0,ena RUN TAB 21 09 2023 13:32:15:299 66744,0:126 1:126,A:3294606329;C:4538635184;G:4708756438;T:3209425450;N:2500743,126,126,,,3294606329,4538635184,4708756438,3209425450,2500743,ERX11454475,ERS16387717,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.8642,0.86388,0.1596,0.16298,0.77051,0.77297,0.7599,0.7352,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14882,ERR12071849,ERX11454474,ERS16387716,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E82 2,SAMEA114399024,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:82 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66741,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 22,82-2_S7_L002_R1_001.fastq.gz 82-2_S7_L002_R2_001.fastq.gz,fastq fastq,20680686684.0,82066217.0,ena RUN TAB 21 09 2023 13:32:15:298 66742,0:126 1:126,A:4358995918;C:5919331822;G:6101024757;T:4296885228;N:4448959,126,126,,,4358995918,5919331822,6101024757,4296885228,4448959,ERX11454474,ERS16387716,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.88722,0.88591,0.1721,0.1755,0.76207,0.76394,0.74661,0.7483,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14883,ERR12071848,ERX11454473,ERS16387715,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,High stress,E82 1,SAMEA114399023,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:82 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:82 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66739,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,82-1_S39_L008_R1_001.fastq.gz 82-1_S39_L008_R2_001.fastq.gz,fastq fastq,19062862812.0,75646281.0,ena RUN TAB 21 09 2023 13:32:15:298 66740,0:126 1:126,A:4015412618;C:5485657253;G:5643544062;T:3914646370;N:3602509,126,126,,,4015412618,5485657253,5643544062,3914646370,3602509,ERX11454473,ERS16387715,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.82331,0.82289,0.14959,0.15262,0.77786,0.77368,0.75014,0.71846,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14884,ERR12071847,ERX11454472,ERS16387714,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E81 5,SAMEA114399022,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:81 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:298 66737,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,81-5_S6_L002_R1_001.fastq.gz 81-5_S6_L002_R2_001.fastq.gz,fastq fastq,14105505960.0,55974230.0,ena RUN TAB 21 09 2023 13:32:15:298 66738,0:126 1:126,A:2867593807;C:4154280778;G:4295901883;T:2784713422;N:3016070,126,126,,,2867593807,4154280778,4295901883,2784713422,3016070,ERX11454472,ERS16387714,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.89055,0.89059,0.15225,0.15462,0.77031,0.7709,0.77204,0.74565,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14885,ERR12071846,ERX11454471,ERS16387713,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E81 4,SAMEA114399021,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:81 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66735,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,81-4_S38_L008_R1_001.fastq.gz 81-4_S38_L008_R2_001.fastq.gz,fastq fastq,14056344540.0,55779145.0,ena RUN TAB 21 09 2023 13:32:15:298 66736,0:126 1:126,A:2941182079;C:4065026103;G:4178339299;T:2869101906;N:2695153,126,126,,,2941182079,4065026103,4178339299,2869101906,2695153,ERX11454471,ERS16387713,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.85089,0.84987,0.16263,0.16502,0.77837,0.77283,0.74931,0.72487,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14886,ERR12071845,ERX11454470,ERS16387712,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E81 2,SAMEA114399020,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:81 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66733,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,81-2_S10_L003_R2_001.fastq.gz 81-2_S10_L003_R1_001.fastq.gz,fastq fastq,12344567004.0,48986377.0,ena RUN TAB 21 09 2023 13:32:15:297 66734,0:126 1:126,A:2564870489;C:3577715066;G:3699995887;T:2500054422;N:1931140,126,126,,,2564870489,3577715066,3699995887,2500054422,1931140,ERX11454470,ERS16387712,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.81332,0.81278,0.14345,0.14595,0.77962,0.78011,0.77642,0.76714,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14887,ERR12071844,ERX11454469,ERS16387711,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E81 1,SAMEA114399019,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:81 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:81 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66731,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,81-1_S2_L001_R1_001.fastq.gz 81-1_S2_L001_R2_001.fastq.gz,fastq fastq,16863847056.0,66920028.0,ena RUN TAB 21 09 2023 13:32:15:297 66732,0:126 1:126,A:3484102096;C:4908704805;G:5083802657;T:3383595635;N:3641863,126,126,,,3484102096,4908704805,5083802657,3383595635,3641863,ERX11454469,ERS16387711,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.90019,0.89959,0.16463,0.16683,0.76607,0.76792,0.76365,0.73132,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14888,ERR12071843,ERX11454468,ERS16387710,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E80 4,SAMEA114399018,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:80 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:297 66729,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,80-4_S9_L003_R1_001.fastq.gz 80-4_S9_L003_R2_001.fastq.gz,fastq fastq,22230539604.0,88216427.0,ena RUN TAB 21 09 2023 13:32:15:297 66730,0:126 1:126,A:4399600032;C:6651638899;G:6855034908;T:4320719496;N:3546269,126,126,,,4399600032,6651638899,6855034908,4320719496,3546269,ERX11454468,ERS16387710,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.84585,0.84448,0.14327,0.14586,0.79078,0.79251,0.79803,0.79459,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14889,ERR12071842,ERX11454467,ERS16387709,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E80 3,SAMEA114399017,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:80 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66727,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,80-3_S1_L001_R2_001.fastq.gz 80-3_S1_L001_R1_001.fastq.gz,fastq fastq,17944230024.0,71207262.0,ena RUN TAB 21 09 2023 13:32:15:296 66728,0:126 1:126,A:3713490828;C:5207225554;G:5378396527;T:3641393155;N:3723960,126,126,,,3713490828,5207225554,5378396527,3641393155,3723960,ERX11454467,ERS16387709,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.84454,0.84386,0.14922,0.15129,0.77264,0.77339,0.75797,0.76206,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14890,ERR12071841,ERX11454466,ERS16387708,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E80 2,SAMEA114399016,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:80 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66725,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,80-2_S5_L002_R1_001.fastq.gz 80-2_S5_L002_R2_001.fastq.gz,fastq fastq,16641238320.0,66036660.0,ena RUN TAB 21 09 2023 13:32:15:296 66726,0:126 1:126,A:3508280857;C:4757668643;G:4898009962;T:3473768461;N:3510397,126,126,,,3508280857,4757668643,4898009962,3473768461,3510397,ERX11454466,ERS16387708,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.86106,0.86111,0.16002,0.16307,0.7653,0.76542,0.72623,0.70444,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14891,ERR12071840,ERX11454465,ERS16387707,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E80 1,SAMEA114399015,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:80 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:80 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66723,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,80-1_S37_L008_R1_001.fastq.gz 80-1_S37_L008_R2_001.fastq.gz,fastq fastq,15269215248.0,60592124.0,ena RUN TAB 21 09 2023 13:32:15:296 66724,0:126 1:126,A:3161128702;C:4439474080;G:4571245477;T:3094451760;N:2915229,126,126,,,3161128702,4439474080,4571245477,3094451760,2915229,ERX11454465,ERS16387707,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.84008,0.83924,0.16203,0.16482,0.78486,0.78301,0.76847,0.76451,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14892,ERR12071839,ERX11454464,ERS16387706,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E115 5,SAMEA114399014,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:115 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:296 66721,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,115-5_S28_L005_R2_001.fastq.gz 115-5_S28_L005_R1_001.fastq.gz,fastq fastq,13704997824.0,54384912.0,ena RUN TAB 21 09 2023 13:32:15:296 66722,0:126 1:126,A:2791048995;C:4040751875;G:4161655954;T:2708992373;N:2548627,126,126,,,2791048995,4040751875,4161655954,2708992373,2548627,ERX11454464,ERS16387706,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.92152,0.922,0.16432,0.16746,0.77977,0.77723,0.7658,0.74319,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14893,ERR12071838,ERX11454463,ERS16387705,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E115 4,SAMEA114399013,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:115 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66719,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,115-4_S73_L007_R1_001.fastq.gz 115-4_S73_L007_R2_001.fastq.gz,fastq fastq,13555374840.0,53791170.0,ena RUN TAB 21 09 2023 13:32:15:295 66720,0:126 1:126,A:2613879041;C:4131073531;G:4251239682;T:2536011431;N:23171155,126,126,,,2613879041,4131073531,4251239682,2536011431,23171155,ERX11454463,ERS16387705,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.93971,0.93992,0.15435,0.15669,0.78766,0.79076,0.76218,0.78676,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14894,ERR12071837,ERX11454462,ERS16387704,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E115 2,SAMEA114399012,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:115 2|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:115 2|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:295 66717,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,115-2_S77_L008_R1_001.fastq.gz 115-2_S77_L008_R2_001.fastq.gz,fastq fastq,19309168872.0,76623686.0,ena RUN TAB 21 09 2023 13:32:15:295 66718,0:126 1:126,A:3659403129;C:5914313547;G:6102556630;T:3596021103;N:36874463,126,126,,,3659403129,5914313547,6102556630,3596021103,36874463,ERX11454462,ERS16387704,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.90206,0.90085,0.164,0.16686,0.81477,0.81856,0.84674,0.83786,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14895,ERR12071835,ERX11454460,ERS16387702,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E114 5,SAMEA114399010,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:114 5|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 5|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66713,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,114-5_S68_L006_R1_001.fastq.gz 114-5_S68_L006_R2_001.fastq.gz,fastq fastq,14161249872.0,56195436.0,ena RUN TAB 21 09 2023 13:32:15:295 66714,0:126 1:126,A:2927386834;C:4098238005;G:4213138034;T:2900333935;N:22153064,126,126,,,2927386834,4098238005,4213138034,2900333935,22153064,ERX11454460,ERS16387702,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.92035,0.91983,0.16785,0.17009,0.75864,0.76292,0.73081,0.75429,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14896,ERR12071834,ERX11454459,ERS16387701,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E114 4,SAMEA114399009,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:114 4|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 4|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66711,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,114-4_S76_L008_R1_001.fastq.gz 114-4_S76_L008_R2_001.fastq.gz,fastq fastq,12939456600.0,51347050.0,ena RUN TAB 21 09 2023 13:32:15:294 66712,0:126 1:126,A:2686900916;C:3725092053;G:3826228928;T:2676529407;N:24705296,126,126,,,2686900916,3725092053,3826228928,2676529407,24705296,ERX11454459,ERS16387701,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.9171,0.91541,0.19718,0.20005,0.76759,0.77285,0.75547,0.75357,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14897,ERR12071833,ERX11454458,ERS16387700,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E114 3,SAMEA114399008,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:114 3|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 3|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66709,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,114-3_S72_L007_R1_001.fastq.gz 114-3_S72_L007_R2_001.fastq.gz,fastq fastq,15510255012.0,61548631.0,ena RUN TAB 21 09 2023 13:32:15:294 66710,0:126 1:126,A:3024458012;C:4641826332;G:4764527525;T:3052903565;N:26539578,126,126,,,3024458012,4641826332,4764527525,3052903565,26539578,ERX11454458,ERS16387700,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.85112,0.84868,0.17054,0.17432,0.79547,0.79851,0.73756,0.8091,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise
14898,ERR12071832,ERX11454457,ERS16387699,ERP151293,PRJEB66218,Social stress in Zebrafish sperm,b81525de-0f4f-4e41-8e34-f411e5590e7b,Other,Environmental changes may affect paternal condition and following generations but the underlying transmission mechanisms of such information is unknown. Male male competition induces a physiological stress response and affects male hormone levels ejaculate traits and hatch rates in their offspring. Here we investigated the potential role of small RNAs in sperm in the transmission of male condition to the next generation. We exposed male zebrafish Danio rerio to high and low male male competition environments for two weeks and collected sperm samples at the end. We also performed IVFs using a split clutch design to distinguish between paternal and maternal effects and collected embryos at 24 hours to test for differentially expressed genes at this key developmental stage. We sequenced mi and piRNAs and the full transcriptome in the resulting offspring and ran a differential expression analyses. We identified differentially expressed sperm mi and piRNAs with the strongest effects observed in sperm of males switching from a high to a low competition environment. We identified 612 differentially expressed genes in the embryos. The changes in gene expression in the embryos support the idea of faster development and hatching and can be linked to some of the differentially expressed small RNAs in sperm.,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,,Low stress,E114 1,SAMEA114399007,University of East Anglia,INSDC center name:University of East Anglia|Submitter Id:114 1|collection date:2014|common name:zebrafish|geographic location country and/or sea:Sweden|sample name:114 1|scientific name:Danio rerio,,,,,,,,,Illumina HiSeq X paired end sequencing,ena EXPERIMENT TAB 21 09 2023 13:32:15:294 66707,125bp,1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X,,ERP151293,Illumina HiSeq X paired end sequencing,ENA FIRST PUBLIC:2023 09 21|ENA LAST UPDATE:2023 09 21,114-1_S27_L005_R1_001.fastq.gz 114-1_S27_L005_R2_001.fastq.gz,fastq fastq,15544755576.0,61685538.0,ena RUN TAB 21 09 2023 13:32:15:294 66708,0:126 1:126,A:3077913021;C:4638218386;G:4760672592;T:3065112184;N:2839393,126,126,,,3077913021,4638218386,4760672592,3065112184,2839393,ERX11454457,ERS16387699,ERA27252154,university of east anglia|European Nucleotide Archive,university of east anglia,2,0.90822,0.90777,0.1775,0.18112,0.79263,0.78808,0.82214,0.79489,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,United Kingdom,2023-09-21,Undetermined,Embryo,Undetermined,Embryo Imprecise