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
71,DRR032753,DRX029559,DRS049958,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 114 individuals,Dr 8cell 2,SAMD00028150,,sample name:Dr 8cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028150,DRX029559,Dr 8cell 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028150,,,,3708921900.0,37089219.0,DRR032753,0:100 1:0,A:985502141;C:874161613;G:869551685;T:979663686;N:42775,100,0,,,985502141,874161613,869551685,979663686,42775,DRX029559,DRS049958,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.93329,,0.02366,,0.78896,,0.47447,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
72,DRR032752,DRX029558,DRS049957,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 96 individuals,Dr 8cell 1,SAMD00028149,,sample name:Dr 8cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028149,DRX029558,Dr 8cell 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028149,,,,3666991200.0,36669912.0,DRR032752,0:100 1:0,A:976118513;C:862559696;G:858017821;T:970254302;N:40868,100,0,,,976118513,862559696,858017821,970254302,40868,DRX029558,DRS049957,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.934,,0.02403,,0.78877,,0.46902,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
86,DRR032738,DRX029544,DRS049943,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 100 individuals,Dr 32cell 2,SAMD00028135,,sample name:Dr 32cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028135,DRX029544,Dr 32cell 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028135,,,,3678713000.0,36787130.0,DRR032738,0:100 1:0,A:981005900;C:863203049;G:859660640;T:974807835;N:35576,100,0,,,981005900,863203049,859660640,974807835,35576,DRX029544,DRS049943,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.93302,,0.02468,,0.77441,,0.47485,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
87,DRR032737,DRX029543,DRS049942,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 95 individuals,Dr 32cell 1,SAMD00028134,,sample name:Dr 32cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028134,DRX029543,Dr 32cell 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028134,,,,3870906500.0,38709065.0,DRR032737,0:100 1:0,A:1030407751;C:909948718;G:905608620;T:1024897443;N:43968,100,0,,,1030407751,909948718,905608620,1024897443,43968,DRX029543,DRS049942,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.93364,,0.02484,,0.77307,,0.47588,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
90,DRR032734,DRX029540,DRS049939,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 107 individuals,Dr 2cell 2,SAMD00028131,,sample name:Dr 2cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028131,DRX029540,Dr 2cell 2,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028131,,,,3687517000.0,36875170.0,DRR032734,0:100 1:0,A:975272080;C:873518282;G:869743434;T:968941851;N:41353,100,0,,,975272080,873518282,869743434,968941851,41353,DRX029540,DRS049939,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.93204,,0.02088,,0.81639,,0.47553,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
91,DRR032733,DRX029539,DRS049938,DRP003810,PRJDB3785,EXPANDE project,DRP003810,Other,EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief  taking advantages of Illumina sequencing  RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.,,,mRNA extracted from pooled embryos of 108 individuals,Dr 2cell 1,SAMD00028130,,sample name:Dr 2cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male  female  and mixed,,,,,,,,,Illumina HiSeq 2000 sequencing of SAMD00028130,DRX029539,Dr 2cell 1,1,Total RNA QIAGEN RNeasy followed by TruSeq,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP003810,Illumina HiSeq 2000 sequencing of SAMD00028130,,,,4156651100.0,41566511.0,DRR032733,0:100 1:0,A:1099943617;C:985498415;G:978884426;T:1092278665;N:45977,100,0,,,1099943617,985498415,978884426,1092278665,45977,DRX029539,DRS049938,DRA003460,"UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo","UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo",1,0.93452,,0.02198,,0.81197,,0.47342,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,Japan,2017-09-20,Cleavage,Embryo,Whole Organism,All anatomical structures
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
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
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
32033,SRR28976522,SRX24505963,SRS21254128,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in IP,GSM8259538,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in IP,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP,GSM8259538,GSM8259538: Zebrafish  RIP seq  Rbm24a Knock in IP; Danio rerio; RIP Seq,GSM8259538 r1,GSM8259538,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz,fastq fastq,6457893104.0,21383752.0,GSM8259538 r1,0:151 1:151,A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968,151,151,,,975588225,2019180290,2469634919,992947702,541968,SRX24505963,SRS21254128,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90304,0.86018,0.20083,0.20471,0.96382,0.96743,0.96102,0.98876,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32034,SRR28976523,SRX24505962,SRS21254127,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type IP,GSM8259537,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type IP,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP,GSM8259537,GSM8259537: Zebrafish  RIP seq  wild type IP; Danio rerio; RIP Seq,GSM8259537 r1,GSM8259537,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz,fastq fastq,4501412680.0,14905340.0,GSM8259537 r1,0:151 1:151,A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621,151,151,,,651609366,1285679784,1901211768,662533141,378621,SRX24505962,SRS21254127,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.96426,0.81361,0.26579,0.2253,0.97784,0.97806,0.8699,0.93379,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32035,SRR28976524,SRX24505961,SRS21254126,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in input,GSM8259536,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in input,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input,GSM8259536,GSM8259536: Zebrafish  RIP seq  Rbm24a Knock in input; Danio rerio; RIP Seq,GSM8259536 r1,GSM8259536,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz,fastq fastq,9539398726.0,31587413.0,GSM8259536 r1,0:151 1:151,A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896,151,151,,,2233069830,2078359171,3009942870,2217201959,824896,SRX24505961,SRS21254126,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90112,0.81448,0.02415,0.01993,0.79287,0.79807,0.47884,0.48186,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32036,SRR28976525,SRX24505960,SRS21254125,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type input,GSM8259535,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type input,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input,GSM8259535,GSM8259535: Zebrafish  RIP seq  wild type input; Danio rerio; RIP Seq,GSM8259535 r1,GSM8259535,1,Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz,fastq fastq,14180410302.0,46955001.0,GSM8259535 r1,0:151 1:151,A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400,151,151,,,3380011534,2883841476,4593876270,3321465622,1215400,SRX24505960,SRS21254125,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.86497,0.64685,0.04432,0.02854,0.79324,0.8031,0.52927,0.53304,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
36993,SRR870737,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f0.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r1,0:76,A:78867584;C:90953343;G:79555524;T:54616280;N:7269,76,,,,78867584,90953343,79555524,54616280,7269,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87907,,0.22745,,0.87117,,0.75368,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36994,SRR870738,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f9.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r10,0:76,A:78816997;C:90959159;G:79657998;T:54558551;N:7295,76,,,,78816997,90959159,79657998,54558551,7295,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.88043,,0.22855,,0.87245,,0.75233,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36995,SRR870739,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f1.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r2,0:76,A:78763536;C:91008400;G:79691191;T:54526580;N:10293,76,,,,78763536,91008400,79691191,54526580,10293,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.8787,,0.22722,,0.87265,,0.72842,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36996,SRR870740,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f2.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r3,0:76,A:78852717;C:90887124;G:79660563;T:54593984;N:5612,76,,,,78852717,90887124,79660563,54593984,5612,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87626,,0.22621,,0.87073,,0.75133,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36997,SRR870741,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f3.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r4,0:76,A:78806910;C:90965443;G:79696522;T:54524188;N:6937,76,,,,78806910,90965443,79696522,54524188,6937,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87542,,0.22492,,0.87334,,0.75289,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36998,SRR870742,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f4.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r5,0:76,A:78982466;C:90858124;G:79522176;T:54631788;N:5446,76,,,,78982466,90858124,79522176,54631788,5446,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87474,,0.22857,,0.87265,,0.75384,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
36999,SRR870743,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f5.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r6,0:76,A:79000082;C:90859539;G:79458519;T:54675434;N:6426,76,,,,79000082,90859539,79458519,54675434,6426,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87608,,0.22983,,0.87203,,0.73363,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37000,SRR870744,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f6.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r7,0:76,A:78895701;C:90912554;G:79599348;T:54584005;N:8392,76,,,,78895701,90912554,79599348,54584005,8392,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87755,,0.2278,,0.87083,,0.75325,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37001,SRR870745,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f7.fastq.gz,fastq,185171644.0,2436469.0,GSM1152439 r8,0:76,A:48221267;C:55301333;G:48330805;T:33315622;N:2617,76,,,,48221267,55301333,48330805,33315622,2617,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87439,,0.22962,,0.87217,,0.76905,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37002,SRR870746,SRX288477,SRS431103,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,GSM1152439,,source name:Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:total RNA,GSM1152439,GSM1152439: Nanog + SoxB1 ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152439,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152439,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPrpf.run1_f8.fastq.gz,fastq,304000000.0,4000000.0,GSM1152439 r9,0:76,A:78852734;C:90938528;G:79608770;T:54594053;N:5915,76,,,,78852734,90938528,79608770,54594053,5915,SRX288477,SRS431103,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.87805,,0.22718,,0.87387,,0.75535,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37003,SRR870734,SRX288476,SRS431104,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,GSM1152438,,source name:Nanog + SoxB1 MO input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,GSM1152438,GSM1152438: Nanog + SoxB1 MO input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152438,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152438,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPinput.run1_f0.fastq.gz,fastq,304000000.0,4000000.0,GSM1152438 r1,0:76,A:83857464;C:80052271;G:74307828;T:64344163;N:1438274,76,,,,83857464,80052271,74307828,64344163,1438274,SRX288476,SRS431104,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90598,,0.19023,,0.75418,,0.68209,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37004,SRR870735,SRX288476,SRS431104,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,GSM1152438,,source name:Nanog + SoxB1 MO input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,GSM1152438,GSM1152438: Nanog + SoxB1 MO input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152438,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152438,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPinput.run1_f1.fastq.gz,fastq,304000000.0,4000000.0,GSM1152438 r2,0:76,A:83962612;C:80121685;G:74457590;T:64429627;N:1028486,76,,,,83962612,80121685,74457590,64429627,1028486,SRX288476,SRS431104,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90513,,0.18947,,0.75272,,0.67499,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37005,SRR870736,SRX288476,SRS431104,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,GSM1152438,,source name:Nanog + SoxB1 MO input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,Nanog + SoxB1 MO input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:Nanog MO  SoxB1 MO|rna subtype:polyA RNA,GSM1152438,GSM1152438: Nanog + SoxB1 MO input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152438,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152438,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,NS2_RPinput.run1_f2.fastq.gz,fastq,160896560.0,2117060.0,GSM1152438 r3,0:76,A:44575257;C:42531891;G:39567390;T:34216932;N:5090,76,,,,44575257,42531891,39567390,34216932,5090,SRX288476,SRS431104,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.91055,,0.1912,,0.75274,,0.66065,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37006,SRR870725,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f0.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r1,0:76,A:73324431;C:87422602;G:80630616;T:62614973;N:7378,76,,,,73324431,87422602,80630616,62614973,7378,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90419,,0.19869,,0.88136,,0.71823,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37007,SRR870726,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f1.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r2,0:76,A:73470482;C:87394958;G:80424001;T:62705138;N:5421,76,,,,73470482,87394958,80424001,62705138,5421,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90116,,0.1987,,0.88318,,0.75079,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37008,SRR870727,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f2.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r3,0:76,A:73282188;C:87383719;G:80721620;T:62606436;N:6037,76,,,,73282188,87383719,80721620,62606436,6037,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90149,,0.19861,,0.88156,,0.74433,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37009,SRR870728,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f3.fastq.gz,fastq,294654812.0,3877037.0,GSM1152437 r4,0:76,A:71307964;C:84655917;G:77925866;T:60760632;N:4433,76,,,,71307964,84655917,77925866,60760632,4433,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90098,,0.19992,,0.88306,,0.75109,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37010,SRR870729,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f4.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r5,0:76,A:73341317;C:87432113;G:80559697;T:62659513;N:7360,76,,,,73341317,87432113,80559697,62659513,7360,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90201,,0.19896,,0.88193,,0.74296,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37011,SRR870730,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f5.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r6,0:76,A:73394014;C:87396975;G:80569514;T:62631217;N:8280,76,,,,73394014,87396975,80569514,62631217,8280,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90195,,0.19918,,0.88288,,0.67362,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37012,SRR870731,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f6.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r7,0:76,A:73414493;C:87403560;G:80487273;T:62688251;N:6423,76,,,,73414493,87403560,80487273,62688251,6423,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.89971,,0.19832,,0.88294,,0.69934,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37013,SRR870732,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f7.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r8,0:76,A:73241313;C:87480362;G:80680397;T:62587911;N:10017,76,,,,73241313,87480362,80680397,62587911,10017,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.9034,,0.19739,,0.88249,,0.73831,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37014,SRR870733,SRX288475,SRS431102,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT ribosome protected fragments for Ribosome Profiling,GSM1152437,,source name:WT ribosome protected fragments for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,WT ribosome protected fragments for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT ribosome protected fragments for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,GSM1152437,GSM1152437: WT ribosome protected fragments for Ribosome Profiling; Danio rerio; OTHER,GSM1152437,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152437,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPrpf.run1_f8.fastq.gz,fastq,304000000.0,4000000.0,GSM1152437 r9,0:76,A:73344291;C:87391219;G:80659159;T:62598862;N:6469,76,,,,73344291,87391219,80659159,62598862,6469,SRX288475,SRS431102,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.89882,,0.19692,,0.88235,,0.71249,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37015,SRR870722,SRX288474,SRS431101,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT input mRNA for Ribosome Profiling,GSM1152436,,source name:WT input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,WT input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,GSM1152436,GSM1152436: WT input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152436,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152436,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPinput.run1_f0.fastq.gz,fastq,304000000.0,4000000.0,GSM1152436 r1,0:76,A:83756699;C:82582873;G:78095254;T:57725687;N:1839487,76,,,,83756699,82582873,78095254,57725687,1839487,SRX288474,SRS431101,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90146,,0.2126,,0.76215,,0.67955,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37016,SRR870723,SRX288474,SRS431101,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT input mRNA for Ribosome Profiling,GSM1152436,,source name:WT input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,WT input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,GSM1152436,GSM1152436: WT input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152436,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152436,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPinput.run1_f1.fastq.gz,fastq,286369292.0,3768017.0,GSM1152436 r2,0:76,A:79362208;C:78237808;G:74048528;T:54711496;N:9252,76,,,,79362208,78237808,74048528,54711496,9252,SRX288474,SRS431101,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90977,,0.21917,,0.76059,,0.67269,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
37017,SRR870724,SRX288474,SRS431101,SRP023492,PRJNA206070,Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition,GSE47558,Other,Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT,,pubmed:24056933,,WT input mRNA for Ribosome Profiling,GSM1152436,,source name:WT input mRNA for Ribosome Profiling|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,WT input mRNA for Ribosome Profiling,Library strategy: Ribosome Profiling Base calling was performed using CASAVA 1.8.2. For mRNA Seq  raw reads were initially filtered by aligning permissively to a ribosomal DNA index and discarded  using Bowtie v0.12.9 with switches   seedlen 25  n 3  k 1  y  e 10000. Unaligned reads were then aligned strand specific to the zebrafish Zv9 UCSC danRer7 genome sequence using Tophat v2.0.7 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 and RefSeq annotations for uniquely aligning reads. Metagenes with names in the form GeneX.GeneY are constructed for reads that do not align uniquely to either gene separately  but align to both genes and nowhere else in the genome. The microRNA miR 430 polycistronic precursor is also listed as a meta gene  called ‘mir 430 hairpin’. RPKMs for gene introns total RNA samples only are similarly calculated  normalizing against the non repetitive sum length of a gene’s introns  and the total number of aligned exonic reads in the sample. For Ribosome Profiling   reads were trimmed of 3’ adapter sequence  and reads in the trimmed length range 28 29nts were retained for ribosome protected fragments  >=18nts for input mRNA. Reads were aligned as above  retaining only uniquely aligned reads to the sense CDS sequences of protein coding genes. Note: traces of exogenous RNA corresponding to a nanog antisense probe  and ntla sense and antisense were detected largely outside the expected size range; these reads were discarded. Gene counts for uniquely aligning reads to CDS regions are listed with respect to RefSeq transcript annotations. Genome build: Ensembl Zv9 / UCSC danRer7 Supplementary files format and content: RPKM tables for exons and introns for mRNA Seq; and RPKM tables for CDS regions for ribosome profiling  generated as described above.,WT input mRNA for Ribosome Profiling,Treated embryos were injected at 1 cell stage for all treatements except cycloheximide  which was applied by bathing 32 cell embryos and incubating at xxxdegreesC.,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,,tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:polyA RNA,GSM1152436,GSM1152436: WT input mRNA for Ribosome Profiling; Danio rerio; OTHER,GSM1152436,,1,For mRNA Seq  total RNA from five embryos was extracted using Trizol Invitrogen for each experimental condition. RNA was treated with TURBO DNase Ambion for 30 minutes at 37°C and extracted using phenol chloroform. For ribosome profiling  50 wild type embryos for each condition were collected at 64 cell stage. Embryos were lysed using 800ul of a mammalian cell lysis buffer containing 100ug/ml Cycloheximide as per the manufacturer’s instruction ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. For nuclease treatment  3ul of ARTseq Nuclease was used. Ribosome protected fragments were run and 28 29nt fragments were gel purified as previously described in Bazzini et al.  2012 and cloned according to the manufacturers protocol ARTseq Ribosome Profiling Kit  RPHMR12126  Epicentre. TruSeq strand specific libraries were constructed according to standard protocols. For total mRNA Seq  sequencing libraries were treated with Epicentre Ribo Zero Gold kits according to the published protocol  in order to deplete ribosomal RNA prior to sequencing. Ribosome profiling libraries were constructed as in Bazzini et al.  Science 2012.,GEO Accession:GSM1152436,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,W2_RPinput.run1_f2.fastq.gz,fastq,304000000.0,4000000.0,GSM1152436 r3,,,,,,,,,,,,SRX288474,SRS431101,SRA082637,GEO,"Giraldez Lab, Genetics, Yale University",1,0.90005,,0.2157,,0.75801,,0.66588,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,United States,2013-05-31,Cleavage,Embryo,Whole Organism,All anatomical structures
40218,SRR2982510,SRX1471511,SRS1197399,SRP067139,PRJNA305418,RiboZero mRNA seq across zebrafish development  for study of uORFs,PRJNA305418,Other,Untranslated mRNA regionsUTRs are key mediators of post transcriptional regulation. Previous studies have predicted thousands of ORFs in five prime'UTRs  the vast majority of which have unknown function. We present a systematic analysis of the translation and function of upstream open reading framesuORFs across vertebrates. Combining high resolution ribosome footprinting and phasing  we find that i uORFs are pervasive within vertebrate transcriptomes  ii the majority show signatures of active translation  and iii uORFs act as potent regulators of translation and RNA levels  with a similar magnitude to miRNAs. Evolution has targeted sequence features to mitigate the effects of constitutively repressive uORFs. Finally  we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.The mRNA seq data contained in this archive were used along with ribosome profiling data to calculate translation efficiency values.,,,,2hpf,AG00244 mrna r0 2h,,strain:TUAB|age:2hpf|sex:pooled male and female|tissue:embryo|genotype:wt|BioSampleModel:Model organism or animal,,,,,,,,,AG00244 mrna r0 2h,2h mRNA R0,1,Twenty embryos per condition were collected from the same clutch from where the ribosome profiling timeseries was conducted.Bazzini et al  2014 Total RNA was isolated using 1mL of Trizol following manufacturer instructions. Ribosomal RNAs were depleted using Ribo Zero Epicentre/Illumina. Strand specific  single end library was constructed according to the Illumina Sample Preparation Kit protocol using standard TruSeq adapters Libraries were prepared and sequenced in an Illumina Hi SEQ  single end  75nt reads,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP067139,,,AG00244_SEQ0039_R1.fastq.gz,fastq,1010085524.0,13290599.0,2h mRNA R0 run1,0:76,A:196715560;C:309406513;G:286228000;T:217670217;N:65234,76,,,,196715560,309406513,286228000,217670217,65234,SRX1471511,SRS1197399,SRA314809,Yale University|Giraldez Lab,Yale University,1,0.89974,,0.14215,,0.79488,,0.72171,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,rrna_depletion,trueseq,bulk,unknown,unknown,,United States,2015-12-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40252,SRR3038046,SRX1494241,SRS1217114,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf preZGA rep3,GSM1976590,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,IgG iCLIP zf preZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNTGGCNN,GSM1976590,GSM1976590: IgG iCLIP zf preZGA rep3; Danio rerio; OTHER,GSM1976590,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976590,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_Drembryo_wt_IgGcontrol_Dr_NNNTGGCNN_20130812_hnRNPA1_4.fq.gz,fastq,600183932.0,7897157.0,GSM1976590 r1,0:76,A:173843237;C:131372689;G:170729621;T:124187689;N:50696,76,,,,173843237,131372689,170729621,124187689,50696,SRX1494241,SRS1217114,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.14511,,0.03659,,0.9332,,0.651,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40253,SRR3038045,SRX1494240,SRS1217115,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf preZGA rep2,GSM1976589,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNCCGGNN,IgG iCLIP zf preZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNCCGGNN,GSM1976589,GSM1976589: IgG iCLIP zf preZGA rep2; Danio rerio; OTHER,GSM1976589,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976589,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_Drembryo_wt_IgGcontrol_Dr_NNNCCGGNN_20130812_hnRNPA1_5.fq.gz,fastq,612280168.0,8056318.0,GSM1976589 r1,0:76,A:175101988;C:144456623;G:172272609;T:120400014;N:48934,76,,,,175101988,144456623,172272609,120400014,48934,SRX1494240,SRS1217115,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.05322,,0.01649,,0.97656,,0.67242,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40254,SRR3038044,SRX1494239,SRS1217116,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,IgG iCLIP zf preZGA rep1,GSM1976588,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,IgG iCLIP zf preZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti IgG|barcode sequence:NNNGGCGNN,GSM1976588,GSM1976588: IgG iCLIP zf preZGA rep1; Danio rerio; OTHER,GSM1976588,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976588,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_IgG_Drembryo_wt_IgGcontrol_Dr_NNNGGCGNN_20130812_hnRNPA1_1.fq-3.gz,fastq,12806760.0,168510.0,GSM1976588 r1,0:76,A:3652525;C:2758781;G:3842061;T:2552042;N:1351,76,,,,3652525,2758781,3842061,2552042,1351,SRX1494239,SRS1217116,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.02784,,0.01181,,0.99813,,0.68217,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40259,SRR3038039,SRX1494234,SRS1217121,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf preZGA rep3,GSM1976583,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,hnRNP A1 iCLIP zf preZGA rep3,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNCAATNN,GSM1976583,GSM1976583: hnRNP A1 iCLIP zf preZGA rep3; Danio rerio; OTHER,GSM1976583,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976583,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_Drembryo_wt_hnRNPA1_Dr_NNNCAATNN_20130812_hnRNPA1_3.fq.gz,fastq,1944912200.0,25590950.0,GSM1976583 r1,0:76,A:611172831;C:390755201;G:517844203;T:424973726;N:166239,76,,,,611172831,390755201,517844203,424973726,166239,SRX1494234,SRS1217121,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.23819,,0.06019,,0.85318,,0.72811,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40260,SRR3038038,SRX1494233,SRS1217122,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf preZGA rep2,GSM1976582,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,hnRNP A1 iCLIP zf preZGA rep2,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNTTGTNN,GSM1976582,GSM1976582: hnRNP A1 iCLIP zf preZGA rep2; Danio rerio; OTHER,GSM1976582,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976582,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_Drembryo_wt_hnRNPA1_Dr_NNNTTGTNN_20130812_hnRNPA1_6.fq.gz,fastq,1804236124.0,23739949.0,GSM1976582 r1,0:76,A:520750722;C:337743522;G:499109535;T:446481275;N:151070,76,,,,520750722,337743522,499109535,446481275,151070,SRX1494233,SRS1217122,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.25184,,0.06217,,0.85687,,0.67912,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
40261,SRR3038037,SRX1494232,SRS1217123,SRP067641,PRJNA306648,Dynamic RNA protein interactions underlie the zebrafish maternal to zygotic transition,GSE76212,Other,We adapted the iCLIP method to zebrafish embryos to investigate activities of Hnrnpa1 during the maternal to zygotic transition Overall design: 3 and 4 biological replicates from zebrafish embryos before preZGA and during ZGA zygotic genome activation  respectively  post UV crosslinking. Negative control samples include 3 IgG replicates of UV crosslinked samples for both developmental stages examined,,pubmed:28381614,,hnRNP A1 iCLIP zf preZGA rep1,GSM1976581,,tissue:zebrafish embryo|developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,hnRNP A1 iCLIP zf preZGA rep1,Basecalls performed using CASAVA version 1.4 For detail on data processing see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959 Genome build: Zv9 version 75 Supplementary files format and content: .bed files describing significant crosslink sites derived from unique contain G in the file name and multi mapped contain M in the file name reads for combined replicates for each individual developmental stages and negative controls.,zebrafish embryo,Zebrafish embryos at the desired developmental stages were irradiated with UV light 254 nm to in vivo crosslink RNA protein interactions.,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,Zebrafish embryos were raised from WT AB strain and maintained using standard conditions.,developmental stage:preZGA 32 cell stage|antibody:anti hnRNP A1|barcode sequence:NNNGGTTNN,GSM1976581,GSM1976581: hnRNP A1 iCLIP zf preZGA rep1; Danio rerio; OTHER,GSM1976581,,1,Zebrafish embryos were lysed and lysates treated with RNaseI to obtain optimal length of RNA fragments for cDNA library preparation. hnRNP A1 RNA complexes were immunopurified using mouse anti hnRNP A1 antibody and protein G dynabeads Invitrogen. Anti IgG antibody Sigma was used for negative control immunopurifications. post RNA dephosphorylation  three prime end linker ligation was performed. Protein RNA complexes were resolved on SDS PAGE and transferred to the nitrocellulose membrane. Region of the membrane above the predicted size of hnRNP A1 was cut and RNA extracted using proteise K treatment. Subsequently  RNA was reverse transcribed using RT primers harboring a barcode. cDNA was separated into three size selected fractions using 6% TBE Urea gel Life Technologies and circularized by ssDNA circligase. Specific oligo was annealed for BamHI restriction site formation. cDNA was linearized by BamHI digestion. Final cDNA libraries were generated by PCR amplification.. For more details see: König et al. 2010: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959,GEO Accession:GSM1976581,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP067641,,,iCLIP_hnRNPA1_Drembryo_wt_hnRNPA1_Dr_NNNGGTTNN_20130812_hnRNPA1_2.fq.gz,fastq,2155200476.0,28357901.0,GSM1976581 r1,0:76,A:646739355;C:394864638;G:606938658;T:506474548;N:183277,76,,,,646739355,394864638,606938658,506474548,183277,SRX1494232,SRS1217123,SRA320959,GEO,"Molecular Biophysics and Biochemistry, Yale University",1,0.24207,,0.05859,,0.84747,,0.70564,,76,,B,,usable mapping rate,illumina,hiseq_era,3prime,other,unknown,bulk,clip,iclip,,United States,2015-12-21,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41556,SRR5017067,SRX2345562,SRS1796129,SRP093295,PRJNA353372,N6 methyladenosine dynamics during early vertebrate embryogenesis,GSE89815,Other,Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages,,,,input 64cell rep2,GSM2390020,,tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type,input 64cell rep2,Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples,Embryos,,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 °C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.,developmental stage:64 cell embryos|strain:AB wild type,GSM2390020,GSM2390020: input 64cell rep2; Danio rerio; RIP Seq,GSM2390020,,1,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,GEO Accession:GSM2390020,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP093295,,,input_64cell_rep2.fastq.gz,fastq,3598782386.0,38284919.0,GSM2390020 r1,0:94,A:953869445;C:864903757;G:875832539;T:903947732;N:228913,94,,,,953869445,864903757,875832539,903947732,228913,SRX2345562,SRS1796129,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04289,,0.00757,,0.9418,,0.6078,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2016-11-14,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41557,SRR5017066,SRX2345561,SRS1796141,SRP093295,PRJNA353372,N6 methyladenosine dynamics during early vertebrate embryogenesis,GSE89815,Other,Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages,,,,input 64cell rep1,GSM2390019,,tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type,input 64cell rep1,Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples,Embryos,,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 °C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.,developmental stage:64 cell embryos|strain:AB wild type,GSM2390019,GSM2390019: input 64cell rep1; Danio rerio; RIP Seq,GSM2390019,,1,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,GEO Accession:GSM2390019,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP093295,,,input_64cell_rep1.fastq.gz,fastq,3538898746.0,37647859.0,GSM2390019 r1,0:94,A:916878511;C:870431252;G:873611680;T:877750503;N:226800,94,,,,916878511,870431252,873611680,877750503,226800,SRX2345561,SRS1796141,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03397,,0.00616,,0.95268,,0.62545,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2016-11-14,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41558,SRR5017065,SRX2345560,SRS1796153,SRP093295,PRJNA353372,N6 methyladenosine dynamics during early vertebrate embryogenesis,GSE89815,Other,Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages,,,,ip 64cell rep2,GSM2390018,,tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type,ip 64cell rep2,Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples,Embryos,,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 °C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.,developmental stage:64 cell embryos|strain:AB wild type,GSM2390018,GSM2390018: ip 64cell rep2; Danio rerio; RIP Seq,GSM2390018,,1,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,GEO Accession:GSM2390018,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP093295,,,ip_64cell_rep2.fastq.gz,fastq,3530677976.0,37560404.0,GSM2390018 r1,0:94,A:966880666;C:841411144;G:858285224;T:862983808;N:1117134,94,,,,966880666,841411144,858285224,862983808,1117134,SRX2345560,SRS1796153,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04775,,0.00421,,0.92845,,0.5748,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2016-11-14,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
41559,SRR5017064,SRX2345559,SRS1796135,SRP093295,PRJNA353372,N6 methyladenosine dynamics during early vertebrate embryogenesis,GSE89815,Other,Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages,,,,ip 64cell rep1,GSM2390017,,tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type,ip 64cell rep1,Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5’end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples,Embryos,,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28±1°C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500µS/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 °C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.,developmental stage:64 cell embryos|strain:AB wild type,GSM2390017,GSM2390017: ip 64cell rep1; Danio rerio; RIP Seq,GSM2390017,,1,We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads® mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3’pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.,GEO Accession:GSM2390017,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP093295,,,ip_64cell_rep1.fastq.gz,fastq,3912003734.0,41617061.0,GSM2390017 r1,0:94,A:1040276279;C:945311584;G:953598043;T:971589029;N:1228799,94,,,,1040276279,945311584,953598043,971589029,1228799,SRX2345559,SRS1796135,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03544,,0.00268,,0.93914,,0.53712,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2016-11-14,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44646,SRR6268202,SRX3374370,SRS2671595,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,oocyte A+ 1h,GSM2845356,,source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte,oocyte A+ 1h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish oocyte,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1h|tissue:oocyte,GSM2845356,GSM2845356: oocyte A+ 1h; Danio rerio; OTHER,GSM2845356,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845356,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR20.fastq.gz,fastq,647004960.0,4043781.0,GSM2845356 r1,0:160 1:0,A:196358573;C:155899107;G:129095192;T:165649225;N:2863,160,0,,,196358573,155899107,129095192,165649225,2863,SRX3374370,SRS2671595,SRA629220,GEO,Broad Institute,1,1e-05,,0.0,,0.99997,,0.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Oocyte,Reproductive System
44649,SRR6268199,SRX3374367,SRS2671602,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,oocyte A  1h,GSM2845353,,source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte,oocyte A  1h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish oocyte,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1h|tissue:oocyte,GSM2845353,GSM2845353: oocyte A  1h; Danio rerio; OTHER,GSM2845353,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845353,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR17-SL38.fastq.gz,fastq,532076160.0,3325476.0,GSM2845353 r1,0:160 1:0,A:162057480;C:125858627;G:108494717;T:135663057;N:2279,160,0,,,162057480,125858627,108494717,135663057,2279,SRX3374367,SRS2671602,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99995,,1.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Oocyte,Reproductive System
44657,SRR6268191,SRX3374359,SRS2671600,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,rep A  2h,GSM2845345,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,rep A  2h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845345,GSM2845345: rep A  2h; Danio rerio; OTHER,GSM2845345,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845345,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,2hpf.fastq.gz,fastq,530420800.0,3315130.0,GSM2845345 r1,0:160 1:0,A:164669564;C:122876218;G:102801422;T:140026363;N:47233,160,0,,,164669564,122876218,102801422,140026363,47233,SRX3374359,SRS2671600,SRA629220,GEO,Broad Institute,1,5e-05,,0.0,,0.99985,,0.71428,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44658,SRR6268190,SRX3374358,SRS2671585,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,rep A  1h,GSM2845344,,source name:zebrafish embryos|developmental stage:1hpf|tissue:embryo,rep A  1h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1hpf|tissue:embryo,GSM2845344,GSM2845344: rep A  1h; Danio rerio; OTHER,GSM2845344,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845344,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,1hpf.fastq.gz,fastq,560763840.0,3504774.0,GSM2845344 r1,0:160 1:0,A:175204436;C:129606168;G:108093534;T:147808098;N:51604,160,0,,,175204436,129606168,108093534,147808098,51604,SRX3374358,SRS2671585,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99995,,0.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44669,SRR6268179,SRX3374347,SRS2671573,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 2h.2,GSM2845333,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,techrep A+ 2h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845333,GSM2845333: techrep A+ 2h.2; Danio rerio; OTHER,GSM2845333,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845333,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR15_S15.fastq.gz,fastq,180869976.0,1076607.0,GSM2845333 r1,0:168 1:0,A:62515123;C:36752824;G:31828965;T:49772532;N:532,168,0,,,62515123,36752824,31828965,49772532,532,SRX3374347,SRS2671573,SRA629220,GEO,Broad Institute,1,1e-05,,0.0,,0.99997,,1.0,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44670,SRR6268178,SRX3374346,SRS2671575,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 1h.2,GSM2845332,,source name:zebrafish embryos|developmental stage:1hpf|tissue:embryo,techrep A+ 1h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1hpf|tissue:embryo,GSM2845332,GSM2845332: techrep A+ 1h.2; Danio rerio; OTHER,GSM2845332,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845332,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR14_S14.fastq.gz,fastq,122214288.0,727466.0,GSM2845332 r1,0:168 1:0,A:42087207;C:24870226;G:21635627;T:33620892;N:336,168,0,,,42087207,24870226,21635627,33620892,336,SRX3374346,SRS2671575,SRA629220,GEO,Broad Institute,1,3e-05,,0.0,,0.99991,,0.25,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44681,SRR6268167,SRX3374335,SRS2671563,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 2h.1,GSM2845321,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,techrep A+ 2h.1,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845321,GSM2845321: techrep A+ 2h.1; Danio rerio; OTHER,GSM2845321,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845321,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR03_S3.fastq.gz,fastq,225004248.0,1339311.0,GSM2845321 r1,0:168 1:0,A:75598393;C:46190266;G:42656101;T:60558836;N:652,168,0,,,75598393,46190266,42656101,60558836,652,SRX3374335,SRS2671563,SRA629220,GEO,Broad Institute,1,1e-05,,0.0,,1.0,,,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44682,SRR6268166,SRX3374334,SRS2671562,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,techrep A+ 1h.1,GSM2845320,,source name:zebrafish embryos|developmental stage:1hpf|tissue:embryo,techrep A+ 1h.1,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1hpf|tissue:embryo,GSM2845320,GSM2845320: techrep A+ 1h.1; Danio rerio; OTHER,GSM2845320,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845320,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,AR02_S2.fastq.gz,fastq,226517928.0,1348321.0,GSM2845320 r1,0:168 1:0,A:75135151;C:47160909;G:43769565;T:60451709;N:594,168,0,,,75135151,47160909,43769565,60451709,594,SRX3374334,SRS2671562,SRA629220,GEO,Broad Institute,1,2e-05,,0.0,,0.99997,,0.0,,168,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44688,SRR6268160,SRX3374328,SRS2671556,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,biorep A+ 1h.2,GSM2845314,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,biorep A+ 1h.2,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845314,GSM2845314: biorep A+ 1h.2; Danio rerio; OTHER,GSM2845314,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845314,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,2hpf_S8.fastq.gz,fastq,404973760.0,2531086.0,GSM2845314 r1,0:160 1:0,A:129717899;C:88023529;G:76695428;T:110511560;N:25344,160,0,,,129717899,88023529,76695428,110511560,25344,SRX3374328,SRS2671556,SRA629220,GEO,Broad Institute,1,3e-05,,0.0,,0.99993,,0.75,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44693,SRR6268155,SRX3374323,SRS2671552,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,biorep A+ 2h.1,GSM2845309,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,biorep A+ 2h.1,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845309,GSM2845309: biorep A+ 2h.1; Danio rerio; OTHER,GSM2845309,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845309,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina MiSeq,,SRP124609,,,2hpf_S1.fastq.gz,fastq,370636000.0,2316475.0,GSM2845309 r1,0:160 1:0,A:119234673;C:80176544;G:68884386;T:102316866;N:23531,160,0,,,119234673,80176544,68884386,102316866,23531,SRX3374323,SRS2671552,SRA629220,GEO,Broad Institute,1,3e-05,,0.0,,0.99995,,1.0,,160,,T,,under 1.2% mapping rate,illumina,miseq,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44702,SRR6268146,SRX3374314,SRS2671543,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,embryo A  2h,GSM2845300,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,embryo A  2h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845300,GSM2845300: embryo A  2h; Danio rerio; OTHER,GSM2845300,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845300,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP124609,,,SPE_0xA_AR03.fastq.gz,fastq,434242100.0,4342421.0,GSM2845300 r1,0:100,A:146151226;C:81755086;G:84240055;T:121992505;N:103228,100,,,,146151226,81755086,84240055,121992505,103228,SRX3374314,SRS2671543,SRA629220,GEO,Broad Institute,1,4e-05,,0.0,,0.99987,,0.16666,,100,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44703,SRR6268145,SRX3374313,SRS2671542,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,embryo A  1h,GSM2845299,,source name:zebrafish embryos|developmental stage:1hpf|tissue:embryo,embryo A  1h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1hpf|tissue:embryo,GSM2845299,GSM2845299: embryo A  1h; Danio rerio; OTHER,GSM2845299,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845299,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP124609,,,SPE_0xA_AR02.fastq.gz,fastq,562608700.0,5626087.0,GSM2845299 r1,0:100,A:184911072;C:108464661;G:112545066;T:156557446;N:130455,100,,,,184911072,108464661,112545066,156557446,130455,SRX3374313,SRS2671542,SRA629220,GEO,Broad Institute,1,4e-05,,0.0,,0.99989,,0.16666,,100,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44712,SRR6268136,SRX3374304,SRS2671534,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,embryo A+ 2h,GSM2845290,,source name:zebrafish embryos|developmental stage:2hpf|tissue:embryo,embryo A+ 2h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:2hpf|tissue:embryo,GSM2845290,GSM2845290: embryo A+ 2h; Danio rerio; OTHER,GSM2845290,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845290,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP124609,,,SPE_40xA_AR03.fastq.gz,fastq,489645300.0,4896453.0,GSM2845290 r1,0:100,A:165413978;C:92119971;G:95310575;T:136699891;N:100885,100,,,,165413978,92119971,95310575,136699891,100885,SRX3374304,SRS2671534,SRA629220,GEO,Broad Institute,1,8e-05,,0.0,,0.99977,,0.45454,,100,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
44713,SRR6268135,SRX3374303,SRS2671532,SRP124609,PRJNA417597,Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation,GSE106677,Other,The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.,,pubmed:29225039,,embryo A+ 1h,GSM2845289,,source name:zebrafish embryos|developmental stage:1hpf|tissue:embryo,embryo A+ 1h,Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5’ terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels,zebrafish embryos,Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.,developmental stage:1hpf|tissue:embryo,GSM2845289,GSM2845289: embryo A+ 1h; Danio rerio; OTHER,GSM2845289,,1,Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors,GEO Accession:GSM2845289,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP124609,,,SPE_40xA_AR02.fastq.gz,fastq,523950900.0,5239509.0,GSM2845289 r1,0:100,A:172597961;C:100919634;G:104852236;T:145471531;N:109538,100,,,,172597961,100919634,104852236,145471531,109538,SRX3374303,SRS2671532,SRA629220,GEO,Broad Institute,1,5e-05,,0.0,,0.99985,,0.14285,,100,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-11-08,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49539,SRR8937005,SRX5717518,SRS4655938,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 2hpf rep2,GSM3732425,,source name:RIP INPUT 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo,RIP INPUT 2hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo,GSM3732425,GSM3732425: RIP INPUT 2hpf rep2; Danio rerio; RIP Seq,GSM3732425,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732425,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_2hpf_rep2_R1.fastq.gz RIP-INPUT_2hpf_rep2_R2.fastq.gz,fastq fastq,16388119500.0,54627065.0,GSM3732425 r1,0:150 1:150,A:3232127065;C:4976385987;G:5052844082;T:3122288663;N:4473703,150,150,,,3232127065,4976385987,5052844082,3122288663,4473703,SRX5717518,SRS4655938,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.98209,0.9812,0.33332,0.33565,0.93811,0.94186,0.95153,0.95984,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49540,SRR8937004,SRX5717517,SRS4655937,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 2hpf rep1,GSM3732424,,source name:RIP INPUT 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo,RIP INPUT 2hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo,GSM3732424,GSM3732424: RIP INPUT 2hpf rep1; Danio rerio; RIP Seq,GSM3732424,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732424,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_2hpf_rep1_R1.fastq.gz RIP-INPUT_2hpf_rep1_R2.fastq.gz,fastq fastq,18857336400.0,62857788.0,GSM3732424 r1,0:150 1:150,A:3116761123;C:6239715125;G:6450542871;T:3049605751;N:711530,150,150,,,3116761123,6239715125,6450542871,3049605751,711530,SRX5717517,SRS4655937,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97874,0.96891,0.03494,0.03355,0.92693,0.93456,0.9502,0.94986,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49543,SRR8937001,SRX5717514,SRS4655934,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 2hpf rep2,GSM3732421,,source name:RIP 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 2hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732421,GSM3732421: RIP 2hpf rep2; Danio rerio; RIP Seq,GSM3732421,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732421,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_2hpf_rep2_R1.fastq.gz RIP_2hpf_rep2_R2.fastq.gz,fastq fastq,17557024800.0,58523416.0,GSM3732421 r1,0:150 1:150,A:4454737772;C:4407385601;G:4364085079;T:4328962997;N:1853351,150,150,,,4454737772,4407385601,4364085079,4328962997,1853351,SRX5717514,SRS4655934,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96216,0.96226,0.08174,0.08009,0.76907,0.77693,0.68824,0.65939,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49544,SRR8937000,SRX5717513,SRS4655933,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 2hpf rep1,GSM3732420,,source name:RIP 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 2hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732420,GSM3732420: RIP 2hpf rep1; Danio rerio; RIP Seq,GSM3732420,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732420,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_2hpf_rep1_R1.fastq.gz RIP_2hpf_rep1_R2.fastq.gz,fastq fastq,5656083600.0,18853612.0,GSM3732420 r1,0:150 1:150,A:1244757394;C:1581273853;G:1666307178;T:1162885398;N:859777,150,150,,,1244757394,1581273853,1666307178,1162885398,859777,SRX5717513,SRS4655933,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.80705,0.80575,0.2454,0.24923,0.85478,0.85644,0.83319,0.80065,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49551,SRR7942634,SRX4776899,SRS3857439,SRP162875,PRJNA493829,m5C profiles in zebrafish embryo sample.,GSE120645,Other,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.,,,,MIX 2hpf m5C rep2,GSM3406900,,source name:Zebrafish embryo and HeLa cell|strain:AB strain and HeLa cell|cell type:Zebrafish embryo and HeLa cell|age:2 hpf|tissue:whole embryo and HeLa cell,MIX 2hpf m5C rep2,Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.,Zebrafish embryo and HeLa cell,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,,strain:AB strain and HeLa cell|cell type:Zebrafish embryo and HeLa cell|age:2 hpf|tissue:whole embryo and HeLa cell,GSM3406900,GSM3406900: MIX 2hpf m5C rep2; Danio rerio; Homo sapiens; OTHER,GSM3406900,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,GEO Accession:GSM3406900,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162875,,,MIX_2hpf_rep2_m5C_R1.fastq.gz MIX_2hpf_rep2_m5C_R2.fastq.gz,fastq fastq,20066397600.0,66887992.0,GSM3406900 r1,0:150 1:150,A:6550429117;C:3498357624;G:3788438779;T:6228759343;N:412737,150,150,,,6550429117,3498357624,3788438779,6228759343,412737,SRX4776899,SRS3857439,SRA786937,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.00028,0.00018,0.00017,8e-05,0.99965,0.99969,0.5,0.5,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-28,Cleavage,Embryo,Whole Organism,All anatomical structures
49552,SRR7942633,SRX4776898,SRS3857438,SRP162875,PRJNA493829,m5C profiles in zebrafish embryo sample.,GSE120645,Other,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.,,,,MIX 2hpf m5C rep1,GSM3406899,,source name:Zebrafish embryo and HeLa cell|strain:AB strain and HeLa cell|cell type:Zebrafish embryo and HeLa cell|age:2 hpf|tissue:whole embryo and HeLa cell,MIX 2hpf m5C rep1,Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.,Zebrafish embryo and HeLa cell,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,,strain:AB strain and HeLa cell|cell type:Zebrafish embryo and HeLa cell|age:2 hpf|tissue:whole embryo and HeLa cell,GSM3406899,GSM3406899: MIX 2hpf m5C rep1; Danio rerio; Homo sapiens; OTHER,GSM3406899,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,GEO Accession:GSM3406899,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162875,,,MIX_2hpf_rep1_m5C_R1.fastq.gz MIX_2hpf_rep1_m5C_R2.fastq.gz,fastq fastq,21831789600.0,72772632.0,GSM3406899 r1,0:150 1:150,A:7043335406;C:3923692693;G:4346641771;T:6517671372;N:448358,150,150,,,7043335406,3923692693,4346641771,6517671372,448358,SRX4776898,SRS3857438,SRA786937,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.00036,0.0003,0.00015,0.00011,0.99935,0.99941,0.69444,0.71875,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-28,Cleavage,Embryo,Whole Organism,All anatomical structures
49561,SRR7942624,SRX4776889,SRS3857429,SRP162875,PRJNA493829,m5C profiles in zebrafish embryo sample.,GSE120645,Other,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.,,,,WT 2hpf m5C rep2,GSM3406890,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:2 hpf|tissue:whole embryo,WT 2hpf m5C rep2,Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.,Zebrafish embryo,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,,strain:AB strain|cell type:Zebrafish embryo|age:2 hpf|tissue:whole embryo,GSM3406890,GSM3406890: WT 2hpf m5C rep2; Danio rerio; OTHER,GSM3406890,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,GEO Accession:GSM3406890,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162875,,,WT_2hpf_rep2_m5C_R1.fastq.gz WT_2hpf_rep2_m5C_R2.fastq.gz,fastq fastq,21717569400.0,72391898.0,GSM3406890 r1,0:150 1:150,A:7289152519;C:3575904987;G:4060222589;T:6790931639;N:1357666,150,150,,,7289152519,3575904987,4060222589,6790931639,1357666,SRX4776889,SRS3857429,SRA786937,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.0016,0.00116,0.00081,0.00044,0.99774,0.99801,0.51333,0.54961,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-28,Cleavage,Embryo,Whole Organism,All anatomical structures
49562,SRR7942623,SRX4776888,SRS3857427,SRP162875,PRJNA493829,m5C profiles in zebrafish embryo sample.,GSE120645,Other,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 µl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. Overall design: Examination of m5C levels in zebrafish embryo.,,,,WT 2hpf m5C rep1,GSM3406889,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:2 hpf|tissue:whole embryo,WT 2hpf m5C rep1,Reads were aligned to the zv9 and hg19 genome assembly using meRanTK v1.2.0 m5C sites were called by meRanCall v1.2.0 and annotated by applying BEDTools’ intersectBed. Genome build: zv9 and hg19 Supplementary files format and content: m5C sites in two biological replicates.,Zebrafish embryo,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer’s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,,strain:AB strain|cell type:Zebrafish embryo|age:2 hpf|tissue:whole embryo,GSM3406889,GSM3406889: WT 2hpf m5C rep1; Danio rerio; OTHER,GSM3406889,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. Thus purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 μl nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer's instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp. RNA BisSeq,GEO Accession:GSM3406889,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162875,,,WT_2hpf_rep1_m5C_R1.fastq.gz WT_2hpf_rep1_m5C_R2.fastq.gz,fastq fastq,23647336500.0,94589346.0,GSM3406889 r1,0:125 1:125,A:7438293574;C:3734712494;G:5516902931;T:6950756730;N:6670771,125,125,,,7438293574,3734712494,5516902931,6950756730,6670771,SRX4776888,SRS3857427,SRA786937,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.00077,0.00016,0.00014,2e-05,0.99829,0.99987,0.48181,0.66666,125,125,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-28,Cleavage,Embryo,Whole Organism,All anatomical structures
49595,SRR7947903,SRX4781859,SRS3862051,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,2h NAIN3 icSHAPE,GSM3409383,,source name:2h NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,2h NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,2h NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,GSM3409383,GSM3409383: 2h NAIN3; Danio rerio; OTHER,GSM3409383,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409383,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,2h_NAIN3_rep1.fastq.gz,fastq,124853039850.0,832353599.0,GSM3409383 r1,0:150 1:0,A:37867788703;C:28959738468;G:28543301824;T:29453073564;N:29137291,150,0,,,37867788703,28959738468,28543301824,29453073564,29137291,SRX4781859,SRS3862051,SRA787572,GEO,"Life Science, Tsinghua University",1,0.03381,,0.00848,,0.94479,,0.68089,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49596,SRR7947904,SRX4781859,SRS3862051,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,2h NAIN3 icSHAPE,GSM3409383,,source name:2h NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,2h NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,2h NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,GSM3409383,GSM3409383: 2h NAIN3; Danio rerio; OTHER,GSM3409383,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409383,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,loader:latf load,2h_NAIN3_rep2.fastq.gz,fastq,159060679200.0,1060404528.0,GSM3409383 r2,0:150 1:0,A:45617471657;C:38274494766;G:38676362132;T:36414708832;N:77641813,150,0,,,45617471657,38274494766,38676362132,36414708832,77641813,SRX4781859,SRS3862051,SRA787572,GEO,"Life Science, Tsinghua University",1,0.03227,,0.01386,,0.96081,,0.70955,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49597,SRR7947901,SRX4781858,SRS3862049,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,2h DMSO icSHAPE,GSM3409382,,source name:2h DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,2h DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,2h DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,GSM3409382,GSM3409382: 2h DMSO; Danio rerio; OTHER,GSM3409382,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409382,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,2h_DMSO_rep1.fastq.gz,fastq,33202617900.0,221350786.0,GSM3409382 r1,0:150 1:0,A:9125761193;C:9027862202;G:7094595163;T:7949637340;N:4762002,150,0,,,9125761193,9027862202,7094595163,7949637340,4762002,SRX4781858,SRS3862049,SRA787572,GEO,"Life Science, Tsinghua University",1,0.05426,,0.01047,,0.92322,,0.74332,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49598,SRR7947902,SRX4781858,SRS3862049,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,2h DMSO icSHAPE,GSM3409382,,source name:2h DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,2h DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,2h DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:2hpf,GSM3409382,GSM3409382: 2h DMSO; Danio rerio; OTHER,GSM3409382,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409382,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,2h_DMSO_rep2.fastq.gz,fastq,48461244300.0,323074962.0,GSM3409382 r2,0:150 1:0,A:14458403614;C:11285495528;G:10770012549;T:11944151781;N:3180828,150,0,,,14458403614,11285495528,10770012549,11944151781,3180828,SRX4781858,SRS3862049,SRA787572,GEO,"Life Science, Tsinghua University",1,0.05259,,0.01006,,0.93206,,0.75282,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49599,SRR7947899,SRX4781857,SRS3862050,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,4 cell NAIN3 icSHAPE,GSM3409381,,source name:4 cell NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,4 cell NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,4 cell NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,GSM3409381,GSM3409381: 4 cell NAIN3; Danio rerio; OTHER,GSM3409381,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409381,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,4-cell_NAIN3_rep1.fastq.gz,fastq,125465584950.0,836437233.0,GSM3409381 r1,0:150 1:0,A:38241494342;C:30192135809;G:25141580458;T:31866971314;N:23403027,150,0,,,38241494342,30192135809,25141580458,31866971314,23403027,SRX4781857,SRS3862050,SRA787572,GEO,"Life Science, Tsinghua University",1,0.02986,,0.00805,,0.9498,,0.69733,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49600,SRR7947900,SRX4781857,SRS3862050,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,4 cell NAIN3 icSHAPE,GSM3409381,,source name:4 cell NAIN3|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,4 cell NAIN3 icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,4 cell NAIN3,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,GSM3409381,GSM3409381: 4 cell NAIN3; Danio rerio; OTHER,GSM3409381,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409381,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,4-cell_NAIN3_rep2.fastq.gz,fastq,124831078200.0,832207188.0,GSM3409381 r2,0:150 1:0,A:37122083059;C:30832904838;G:28247183546;T:28612305554;N:16601203,150,0,,,37122083059,30832904838,28247183546,28612305554,16601203,SRX4781857,SRS3862050,SRA787572,GEO,"Life Science, Tsinghua University",1,0.04217,,0.01947,,0.95542,,0.71549,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49601,SRR7947897,SRX4781856,SRS3862048,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,4 cell DMSO icSHAPE,GSM3409380,,source name:4 cell DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,4 cell DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,4 cell DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,GSM3409380,GSM3409380: 4 cell DMSO; Danio rerio; OTHER,GSM3409380,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409380,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,4-cell_DMSO_rep1.fastq.gz,fastq,36427183500.0,242847890.0,GSM3409380 r1,0:150 1:0,A:10144008700;C:9612700528;G:7003058984;T:9662936070;N:4479218,150,0,,,10144008700,9612700528,7003058984,9662936070,4479218,SRX4781856,SRS3862048,SRA787572,GEO,"Life Science, Tsinghua University",1,0.02972,,0.00598,,0.94998,,0.74592,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
49602,SRR7947898,SRX4781856,SRS3862048,SRP163087,PRJNA494251,Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis,GSE120724,Other,We resolved the RNA secondary structure during zebrafish early embryogenesis based on  in vivo click selective 2' hydroxyl acylation and profiling experiment icSHAPE. We analyzed the RNA structure dynamics among different development stages.  Also  we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages  including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA seq of 6 samples from zebrafish embryos at 2  4  6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP seq of 4 samples from flag elavl1a mRNA injected zebrafish embryos at xxx and 6 h.p.f. including two biological replicates.,,pubmed:32423473,,4 cell DMSO icSHAPE,GSM3409380,,source name:4 cell DMSO|strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,4 cell DMSO icSHAPE,Library strategy: icSHAPE icSHAPE computational pipeline reference: PubMedID: 26766114  DOI: 10.1038/nprot.2016.011 trimmed three prime adaptor from reads by cutadapt trimmed low quality bases by trimmomatic collapsed duplicated reads as icSHAPE pipeline trimmed the leading 13nt UMI mapping reads to zebrafish reference transcriptomez10 by bowtie2 using the same parameters in icSHAPE pipeline calculate rpkm as icshape pipeline calculate reverse transcription stop sitesRT stop as icshape pipeline RT stop was normalized by using sliding window  then icSHAPE score was calculated as icshape pipeline Genome build: z10 Supplementary files format and content: tab delimited text files for icshape files. First column is the Refseq ID  second is transcript length  third is RPKM  then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. Tab delimited text files for read counts and rpkm files. First column is the Refseq ID  second is  transcript length  third is the unique mapped reads count  fourth is the mulitple mapped reads count  fifth is the RPKM.,4 cell DMSO,For in vivo treatment  cells was incubated with NAI N3 or DMSO at 28.5  C for 5min.,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen.To enrich polyA RNA  the total RNA was subjected to polyA selection. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before 3’ adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM 5’ adenylated and 3’ blocked linker 3’ bio for unmodified  3’ ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl 5’ Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer’s protocol.,Zebrafish wild type strain AB was raised in system water at 28.5°C under standard conditions.,strain:AB|tissue:zebrafish embryos|genotype/variation:normal zebrafish embryos cells|age:1hpf,GSM3409380,GSM3409380: 4 cell DMSO; Danio rerio; OTHER,GSM3409380,,1,The  RNA or modified RNA was extracted or cleaned up and eluted in RNase free water by using TRIzol® Reagent invitrogen. For icSHAPE  the in vivo modified RNA and unmodified RNA were biotinylated by copper free click reaction  followed by fragmentation. The fragmented RNA was end repaired by incubation at 37°C for 1 hours with the following mix 70 mM Tris 7.0  18mM MgCl2  5mM DTT  4 U/µl RiboLock  0.1 U/µl FastAP Life Technology  2 U/µl T4 PNKNEB before three prime adapter ligation with addition of 10 µl ligation mix 5mM DTT  0.5µM five prime adenylated and three prime blocked linker three prime bio for unmodified  three prime ddc for modified  0.66 U/µl T4 RNA ligase NEB  M0437M  15% PEG8000  1X RNA ligase buffer and incubation at 25°C for extra 3 hours. Then the excess adaptor was removed as described below. The purified RNA was incubated in the mix of 1µl FastAP  0.2µl SSB Promega  0.8µl Ribolock and 1µl five prime Deadenylase NEB in 1X NEB buffer 2 NEB at 30°C for 90 min. And then 1µl RecJf NEB was added with another incubation at 37°C for 1 hour. The following procedures  including reverse transcription  biotin streptavadin enrichment  size selection of cDNA  circularization and PCR amplification  were the same as described in the standard protocol. For RNA seq， Fragmented mRNA was used for library construction using the KAPA Stranded mRNA Seq Kit KAPA according to manufacturer's protocol.,GEO Accession:GSM3409380,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP163087,,,4-cell_DMSO_rep2.fastq.gz,fastq,29467554900.0,196450366.0,GSM3409380 r2,0:150 1:0,A:8423294297;C:7531918888;G:6038081539;T:7471822550;N:2437626,150,0,,,8423294297,7531918888,6038081539,7471822550,2437626,SRX4781856,SRS3862048,SRA787572,GEO,"Life Science, Tsinghua University",1,0.04597,,0.00671,,0.93003,,0.68348,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,clip,iclip,,China,2018-10-01,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56351,SRR10948881,SRX7615939,SRS6049198,SRP243873,PRJNA602610,Global promoter usage in the differentfractions of the cell during early zebrafish development,GSE144040,Other,We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome   Shield and Prim 5 stages of development.,,pubmed:33795334,,64Cell Cyt CAGE,GSM4278487,,source name:64Cell stage embryo|tissue:zebrafish embryos|Stage:64Cell|fraction:Cytosolic|molecule type:capped RNAs,64Cell Cyt CAGE,Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering  normalization  removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al.  2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|Stage:64Cell|fraction:Cytosolic|molecule type:capped RNAs,GSM4278487,GSM4278487: 64Cell Cyt CAGE; Danio rerio; OTHER,GSM4278487,,1,RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,GEO Accession:GSM4278487,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP243873,,,Cell64_Cyt_L006_R1_001.fastq.gz Cell64_Cyt_L006_R2_001.fastq.gz,fastq fastq,166574140.0,1753412.0,GSM4278487 r1,0:51 1:44,A:34424987;C:43748779;G:47831884;T:40564939;N:3551,51,44,,,34424987,43748779,47831884,40564939,3551,SRX7615939,SRS6049198,SRA1029879,GEO,"School of Biosciences, University of Birmingham",2,0.94853,0.36859,0.20547,0.07164,0.80377,0.84845,0.66429,0.60646,51,44,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,5prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2020-01-22,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
56352,SRR10948880,SRX7615938,SRS6049197,SRP243873,PRJNA602610,Global promoter usage in the differentfractions of the cell during early zebrafish development,GSE144040,Other,We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome   Shield and Prim 5 stages of development.,,pubmed:33795334,,64Cell Nuc CAGE,GSM4278486,,source name:64Cell stage embryo|tissue:zebrafish embryos|Stage:64Cell|fraction:Nuclear|molecule type:capped RNAs,64Cell Nuc CAGE,Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering  normalization  removal of the additional 5’ end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al.  2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format,64Cell stage embryo,Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 µL of RLN buffer and finally  collected and labelled as the nuclear fraction.,RNA was extracted using the Rneasy mini kit The conventional method used for 5’ cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the 5’ end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.,tissue:zebrafish embryos|Stage:64Cell|fraction:Nuclear|molecule type:capped RNAs,GSM4278486,GSM4278486: 64Cell Nuc CAGE; Danio rerio; OTHER,GSM4278486,,1,RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.,GEO Accession:GSM4278486,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP243873,,,Cell64_Nuc_L006_R1_001.fastq.gz Cell64_Nuc_L006_R2_001.fastq.gz,fastq fastq,254581570.0,2679806.0,GSM4278486 r1,0:51 1:44,A:53351059;C:66480035;G:73184710;T:61560147;N:5619,51,44,,,53351059,66480035,73184710,61560147,5619,SRX7615938,SRS6049197,SRA1029879,GEO,"School of Biosciences, University of Birmingham",2,0.85142,0.32881,0.18708,0.06992,0.7864,0.84159,0.62224,0.57075,51,44,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,5prime,other,unknown,bulk,unknown,unknown,,United Kingdom,2020-01-22,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
59499,SRR11924325,SRX8469997,SRS6770648,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,small RNA 32 cell,GSM4591064,,source name:32 cell stage|tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,small RNA 32 cell,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,,tissue:32 cell stage|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt,GSM4591064,GSM4591064: small RNA 32 cell; Danio rerio; OTHER,GSM4591064,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction  one  ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen  and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short  the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs  adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module  without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.,GEO Accession:GSM4591064,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent S5,,SRP265951,,,small_RNA_32_cell_stage.fastq,fastq,275040056.0,6091077.0,GSM4591064 r1,0:45.15,A:69136092;C:69806677;G:72527986;T:63569301;N:0,45,,,,69136092,69806677,72527986,63569301,0,SRX8469997,SRS6770648,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.67676,,0.30881,,0.86636,,0.63482,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,rrna_depletion,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59509,SRR11924311,SRX8469986,SRS6770637,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 3,GSM4591054,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 3,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591054,GSM4591054: 32 cell 3; Danio rerio; OTHER,GSM4591054,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591054,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_3.bam GSE151797_Reference_sequence.fa,bam bam,306452866.0,9472058.0,GSM4591054 r1,0:32.35,A:62923439;C:99486553;G:78734118;T:65308756;N:0,32,,,,62923439,99486553,78734118,65308756,0,SRX8469986,SRS6770637,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.69616,,0.21356,,0.91885,,0.77399,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59510,SRR11924310,SRX8469985,SRS6770636,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 2,GSM4591053,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591053,GSM4591053: 32 cell 2; Danio rerio; OTHER,GSM4591053,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591053,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_2.bam GSE151797_Reference_sequence.fa,bam bam,231900531.0,6985149.0,GSM4591053 r1,0:33.20,A:46033127;C:77390842;G:61355372;T:47121190;N:0,33,,,,46033127,77390842,61355372,47121190,0,SRX8469985,SRS6770636,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.83429,,0.25864,,0.9137,,0.78928,,39,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
59511,SRR11924308,SRX8469984,SRS6770635,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,32 cell 1,GSM4591052,,source name:32 cell stage|tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,32 cell 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,32 cell stage,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:32 cell stage|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591052,GSM4591052: 32 cell 1; Danio rerio; OTHER,GSM4591052,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591052,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,32_cell_1.bam GSE151797_Reference_sequence.fa,bam bam,252107732.0,7470443.0,GSM4591052 r1,0:33.75,A:53056857;C:79089015;G:65131744;T:54830116;N:0,33,,,,53056857,79089015,65131744,54830116,0,SRX8469984,SRS6770635,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.78874,,0.25062,,0.89645,,0.73533,,48,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Cleavage,Embryo,Undetermined,Embryo Imprecise
63732,SRR13998080,SRX10375446,SRS8490052,SRP311218,PRJNA715461,RIP seq for Ddx3xb in zebrafish embryos,GSE169161,Other,We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates,parent bioproject:PRJNA715459,pubmed:35661831,,rip 2h WT rep2,GSM5179332,,source name:control 2h RIP seq rep2|tissue:zebrafish embryos|genotype:wild type|age:2 hpf,rip 2h WT rep2,low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 2h RIP seq rep2,,flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.,,tissue:zebrafish embryos|genotype:wild type|age:2 hpf,GSM5179332,GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq,GSM5179332,,1,RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc,GEO Accession:GSM5179332,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP311218,,loader:fastq load.py,rip_2h_WT2.fq.gz,fastq,12320805000.0,82138700.0,GSM5179332 r1,0:150,A:3686415626;C:2826613772;G:3732955088;T:2073945227;N:875287,150,,,,3686415626,2826613772,3732955088,2073945227,875287,SRX10375446,SRS8490052,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.1848,,0.11194,,0.9669,,0.82171,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,China,2021-03-18,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
63733,SRR13998079,SRX10375445,SRS8490051,SRP311218,PRJNA715461,RIP seq for Ddx3xb in zebrafish embryos,GSE169161,Other,We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates,parent bioproject:PRJNA715459,pubmed:35661831,,rip 2h WT rep1,GSM5179331,,source name:control 2h RIP seq rep1|tissue:zebrafish embryos|genotype:wild type|age:2 hpf,rip 2h WT rep1,low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 2h RIP seq rep1,,flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.,,tissue:zebrafish embryos|genotype:wild type|age:2 hpf,GSM5179331,GSM5179331: rip 2h WT rep1; Danio rerio; RIP Seq,GSM5179331,,1,RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc,GEO Accession:GSM5179331,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP311218,,loader:fastq load.py,rip_2h_WT1.fq.gz,fastq,8787958800.0,58586392.0,GSM5179331 r1,0:150,A:2671043775;C:2046825976;G:2545406298;T:1524056303;N:626448,150,,,,2671043775,2046825976,2545406298,1524056303,626448,SRX10375445,SRS8490051,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.30731,,0.17665,,0.94117,,0.79653,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,China,2021-03-18,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
69409,SRR18516952,SRX14648010,SRS12413415,SRP366502,PRJNA821148,CAGE seq total and nuclear RNA and nanT iCAGE acrosss 6 developmental stages,PRJNA821148,Other,In order to compare mRNA expression in the whole cell and the nucleus during development  we prepared CAGE seq libraries from total RNA as well as only from nuclear RNA as well as nanti CAGE on 6 developmental stages,,,,,DCD007419BS,,strain:AB|age:1.5hpf|dev stage:16 cell|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|BioSampleModel:Model organism or animal,,,,,,,,,nanT iCAGE 16 cell,DCD003632SQ,DCD003632SQ,nanT iCAGE with Total RNA  max read depth: 48,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP366502,,,CAGE-seq_Mueller_lab_0008AS.DCD003632SQ.USERirene.stevens.R1.fastq.gz,fastq,392835168.0,8184066.0,CAGE seq Mueller lab 0008AS.DCD003632SQ.USERirene.stevens.R1.fastq.gz,0:48 1:0,A:106127709;C:94140127;G:103587770;T:88439881;N:539681,48,0,,,106127709,94140127,103587770,88439881,539681,SRX14648010,SRS12413415,SRA1393751,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.87892,,0.18576,,0.80509,,0.63419,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
69410,SRR18516953,SRX14648009,SRS12413415,SRP366502,PRJNA821148,CAGE seq total and nuclear RNA and nanT iCAGE acrosss 6 developmental stages,PRJNA821148,Other,In order to compare mRNA expression in the whole cell and the nucleus during development  we prepared CAGE seq libraries from total RNA as well as only from nuclear RNA as well as nanti CAGE on 6 developmental stages,,,,,DCD007419BS,,strain:AB|age:1.5hpf|dev stage:16 cell|sex:not applicable|tissue:early embryonic cell|biomaterial provider:Mueller lab  University of Birmingham|BioSampleModel:Model organism or animal,,,,,,,,,nanT iCAGE 16 cell,DCD003637SQ,DCD003637SQ,nanT iCAGE with Total RNA  max read depth: 48,,,RNA-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP366502,,,CAGE-seq_Mueller_lab_0008AS.DCD003637SQ.USERirene.stevens.R1.fastq.gz,fastq,225142368.0,4690466.0,CAGE seq Mueller lab 0008AS.DCD003637SQ.USERirene.stevens.R1.fastq.gz,0:48 1:0,A:61697148;C:52348969;G:58818293;T:51968512;N:309446,48,0,,,61697148,52348969,58818293,51968512,309446,SRX14648009,SRS12413415,SRA1393751,DANIO-CODE|Department for Biosciences and Nutrition,DANIO-CODE DANIO-CODE,1,0.8438,,0.1185,,0.78476,,0.66042,,48,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,Unknown,2022-03-29,Cleavage,Embryo,Embryo Imprecise,All anatomical structures
75633,SRR24746216,SRX20523363,SRS17832951,SRP439774,PRJNA976671,RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos,GSE233570,Other,To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.,,pubmed:38177902,,eIF4E1c input biol rep 3,GSM7430668,,source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c|geo loc name:missing|collection date:missing,eIF4E1c input biol rep 3,RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts,Whole embryo lysate,,RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro,,tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c,GSM7430668,GSM7430668: eIF4E1c input biol rep 3; Danio rerio; RIP Seq,GSM7430668 r1,GSM7430668,1,RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP439774,,loader:fastq load.py,e1c-RIP_input_3_1.fastq.gz e1c-RIP_input_3_2.fastq.gz,fastq fastq,3690634738.0,18270469.0,GSM7430668 r1,0:101 1:101,A:844997958;C:941209221;G:1016802233;T:887576626;N:48700,101,101,,,844997958,941209221,1016802233,887576626,48700,SRX20523363,SRS17832951,SRA1645065,IMP,IMP,2,0.88478,0.85242,0.07667,0.0787,0.77354,0.77636,0.54943,0.5474,101,101,B,B,biological fallback assumption,illumina,novaseq_era,full_length,rrna_depletion,ribozero,bulk,unknown,unknown,,Austria,2023-05-26,Cleavage,Embryo,Whole Organism,All anatomical structures