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166 rows where devstage_curation = "Cleavage" and experiment.library_strategy = "OTHER"

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  • OTHER · 166 ✖

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  • Cleavage · 166 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9742 9742 ERR3489868 ERX3511283 ERS3556003 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 4Ei 10 SAMEA5752544 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 20 64 cell 4Ei 10 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     5928054796.0 78000721.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 20 0:76 A:2109854905;C:1377083508;G:1616166285;T:824889630;N:60468 76       2109854905 1377083508 1616166285 824889630 60468 ERX3511283 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61525   0.45233   0.99379   0.57373   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9743 9743 ERR3489867 ERX3511282 ERS3556003 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 4Ei 10 SAMEA5752544 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 19 64 cell 4Ei 10 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     9772604780.0 128586905.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 19 0:76 A:3901301079;C:2223067879;G:2553338016;T:1094797648;N:100158 76       3901301079 2223067879 2553338016 1094797648 100158 ERX3511282 ERS3556003 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.52103   0.25046   0.9861   0.64575   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9744 9744 ERR3489866 ERX3511281 ERS3556002 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 4Ei 0.1 SAMEA5752543 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 18 64 cell 4Ei 0.1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26     6730725680.0 88562180.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 18 0:76 A:3805722011;C:1188715051;G:1382258076;T:353814168;N:216374 76       3805722011 1188715051 1382258076 353814168 216374 ERX3511281 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.61922   0.37217   0.99527   0.29148   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9745 9745 ERR3489865 ERX3511280 ERS3556002 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 4Ei 0.1 SAMEA5752543 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752543|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:6|common name:zebrafish|dev stage:64 cell|sample name:6|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 17 64 cell 4Ei 0.1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 09 26     10616304872.0 139688222.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 17 0:76 A:4717003484;C:2600725234;G:2586105174;T:712124440;N:346540 76       4717003484 2600725234 2586105174 712124440 346540 ERX3511280 ERS3556002 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.30908   0.08252   0.94683   0.69548   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9758 9758 ERR3489852 ERX3511267 ERS3555998 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 2 SAMEA5752539 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 4 64 cell 2 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     11722578884.0 154244459.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 4 0:76 A:8175036829;C:1396062240;G:1882846539;T:268587131;N:46145 76       8175036829 1396062240 1882846539 268587131 46145 ERX3511267 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.81133   0.41331   0.99823   0.03453   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9759 9759 ERR3489851 ERX3511266 ERS3555998 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 2 SAMEA5752539 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 3 64 cell 2 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     9525478088.0 125335238.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 3 0:76 A:4813606784;C:2048902072;G:2140220088;T:522714000;N:35144 76       4813606784 2048902072 2140220088 522714000 35144 ERX3511266 ERS3555998 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.59747   0.26784   0.996   0.21193   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9760 9760 ERR3489850 ERX3511265 ERS3555997 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 1 SAMEA5752538 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 2 64 cell 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     8544157652.0 112423127.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 2 0:76 A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086 76       2633354802 2582123846 2505786164 822713754 179086 ERX3511265 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34707   0.02129   0.99797   0.62478   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9761 9761 ERR3489849 ERX3511264 ERS3555997 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 1 SAMEA5752538 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 1 64 cell 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22 run7_64_cell_SSU_12_13_14.fastq.gz fastq 10139466432.0 133414032.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 1 0:76 1:0 A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884 76 0     4628193785 2494821868 2485640988 530605907 203884 ERX3511264 ERS3555997 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06893   0.02559   0.99766   0.90567   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9762 9762 ERR3413870 ERX3437516 ERS3555997 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 1 SAMEA5752538 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 2 64 cell 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     8544157652.0 112423127.0 ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 2 0:76 A:2633354802;C:2582123846;G:2505786164;T:822713754;N:179086 76       2633354802 2582123846 2505786164 822713754 179086 ERX3437516 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.34696   0.02086   0.99795   0.66261   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9763 9763 ERR3413869 ERX3437515 ERS3555997 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 1 SAMEA5752538 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 03 07 2019 14:45:09:705 1 64 cell 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     10139466432.0 133414032.0 ena RUN Computational Biology Unit 03 07 2019 14:45:09:705 1 0:76 A:4628193785;C:2494821868;G:2485640988;T:530605907;N:203884 76       4628193785 2494821868 2485640988 530605907 203884 ERX3437515 ERS3555997 ERA2028987 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.06884   0.02526   0.99762   0.89856   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
29229 29229 SRR27489746 SRX23160963 SRS20111121 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica C MPRA repC fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica C Library 36 Library 36 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz fastq fastq 13085558528.0 43329664.0 BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985 151 151     3305413622 3391845548 3249932870 3137708503 657985 SRX23160963 SRS20111121 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01098 8e-05 0.00025 0.0 0.99216 0.99973 0.4317 0.61538 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29230 29230 SRR27489747 SRX23160962 SRS20111119 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica C MPRA repC fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica C Library 35 Library 35 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz fastq fastq 16647721914.0 55124907.0 BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108 151 151     4231542934 4348688006 4050131444 4016534422 825108 SRX23160962 SRS20111119 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01514 0.00017 0.00035 3e-05 0.99109 0.99955 0.4372 0.30434 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29231 29231 SRR27489748 SRX23160961 SRS20111118 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica C MPRA repC fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica C Library 34 Library 34 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz fastq fastq 15431181052.0 51096626.0 BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999 151 151     3856018869 4036338306 3877988553 3660059325 775999 SRX23160961 SRS20111118 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01114 8e-05 0.00028 0.0 0.99192 0.99975 0.42956 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29232 29232 SRR27489749 SRX23160960 SRS20111117 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica C MPRA repC input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 2hpf replica C Library 33 Library 33 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz fastq fastq 11771229160.0 38977580.0 BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080 151 151     2999574420 3115525474 2806539264 2849003922 586080 SRX23160960 SRS20111117 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01997 2e-05 0.00054 0.0 0.99022 0.99993 0.41853 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29235 29235 SRR27489752 SRX23160957 SRS20111114 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica A MPRA repA fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica A Library 4 Library 4 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz fastq fastq 12108626278.0 40094789.0 BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268 151 151     3079403604 3149095123 2953175005 2926352278 600268 SRX23160957 SRS20111114 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.014 5e-05 0.00032 0.0 0.99137 0.99987 0.45127 0.28571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29246 29246 SRR27489763 SRX23160946 SRS20111108 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica A MPRA repA fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica A Library 3 Library 3 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz fastq fastq 12524202136.0 41470868.0 BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842 151 151     3168466372 3269998328 3075956662 3009160932 619842 SRX23160946 SRS20111108 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01351 7e-05 0.00028 0.0 0.99168 0.99977 0.43472 0.54545 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29247 29247 SRR27489764 SRX23160945 SRS20111103 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica B MPRA repB fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica B Library 20 Library 20 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz fastq fastq 12514444214.0 41438557.0 BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303 151 151     3174354240 3246812350 3082021359 3010633962 622303 SRX23160945 SRS20111103 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01121 0.00016 0.00027 1e-05 0.99204 0.99953 0.43533 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29248 29248 SRR27489765 SRX23160944 SRS20111102 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica B MPRA repB fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica B Library 19 Library 19 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz fastq fastq 16535129670.0 54752085.0 BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421 151 151     4184643114 4312135767 4051628900 3985895468 826421 SRX23160944 SRS20111102 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01416 0.00017 0.00031 1e-05 0.9917 0.99941 0.40732 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29249 29249 SRR27489766 SRX23160943 SRS20111101 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica B MPRA repB fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica B Library 18 Library 18 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz fastq fastq 12692870042.0 42029371.0 BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284 151 151     3179006274 3325152682 3173386021 3014687781 637284 SRX23160943 SRS20111101 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01199 8e-05 0.0003 1e-05 0.99145 0.99979 0.40897 0.36363 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29250 29250 SRR27489767 SRX23160942 SRS20111100 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica B MPRA repB input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 2hpf replica B Library 17 Library 17 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz fastq fastq 13169436008.0 43607404.0 BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755 151 151     3341908647 3485072739 3171200836 3170595031 658755 SRX23160942 SRS20111100 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01868 5e-05 0.0006 0.0 0.99038 0.99983 0.41955 0.125 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29257 29257 SRR27489774 SRX23160935 SRS20111093 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica A MPRA repA fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica A Library 2 Library 2 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz fastq fastq 16111078182.0 53347941.0 BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034 151 151     4069536779 4222816450 3957789955 3860129964 805034 SRX23160935 SRS20111093 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01511 5e-05 0.00034 0.0 0.99135 0.99985 0.41564 0.42857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29258 29258 SRR27489775 SRX23160934 SRS20111092 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica A MPRA repA input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 2hpf replica A Library 1 Library 1 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz fastq fastq 9769305890.0 32348695.0 BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485 151 151     2477269774 2598109179 2338444856 2354997596 484485 SRX23160934 SRS20111092 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0205 4e-05 0.00059 0.0 0.99013 0.99987 0.41957 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29743 29743 SRR27467676 SRX23139230 SRS20090273 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep2 EV04004 EV04004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04004.R1.fastq.gz fastq 895671560.0 6397654.0 EV04004.R1.fastq.gz 0:140 A:206443066;C:147067097;G:365386937;T:176734600;N:39860 140       206443066 147067097 365386937 176734600 39860 SRX23139230 SRS20090273 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29744 29744 SRR27467677 SRX23139229 SRS20090274 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep2 EV04003 EV04003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04003.R1.fastq.gz fastq 664112120.0 4743658.0 EV04003.R1.fastq.gz 0:140 A:163711695;C:142612940;G:211194350;T:146562626;N:30509 140       163711695 142612940 211194350 146562626 30509 SRX23139229 SRS20090274 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29758 29758 SRR27437478 SRX23109819 SRS20064573 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep3 EV07006 EV07006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07006.R1.fastq.gz fastq 2584527680.0 18460912.0 EV07006.R1.fastq.gz 0:140 A:685107500;C:367766834;G:717359848;T:814224206;N:69292 140       685107500 367766834 717359848 814224206 69292 SRX23109819 SRS20064573 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   1e-05   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29759 29759 SRR27437479 SRX23109818 SRS20064571 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep3 EV07005 EV07005 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07005.R1.fastq.gz fastq 713829480.0 5098782.0 EV07005.R1.fastq.gz 0:140 A:183575304;C:168886779;G:213156258;T:148191838;N:19301 140       183575304 168886779 213156258 148191838 19301 SRX23109818 SRS20064571 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 5e-05   0.0   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29760 29760 SRR27437480 SRX23109817 SRS20064572 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep3 EV07004 EV07004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07004.R1.fastq.gz fastq 517336680.0 3695262.0 EV07004.R1.fastq.gz 0:140 A:136783049;C:131207858;G:139873280;T:109458276;N:14217 140       136783049 131207858 139873280 109458276 14217 SRX23109817 SRS20064572 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 7e-05   0.0   0.99981   0.7   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29779 29779 SRR27435864 SRX23108232 SRS20063068 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep4 EV08009 EV08009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08009.R1.fastq.gz fastq 756964460.0 5406889.0 EV08009.R1.fastq.gz 0:140 A:191381054;C:111783194;G:185694475;T:268052883;N:52854 140       191381054 111783194 185694475 268052883 52854 SRX23108232 SRS20063068 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29780 29780 SRR27435865 SRX23108231 SRS20063069 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep4 EV08008 EV08008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08008.R1.fastq.gz fastq 751794680.0 5369962.0 EV08008.R1.fastq.gz 0:140 A:194845808;C:197389162;G:194749636;T:164756481;N:53593 140       194845808 197389162 194749636 164756481 53593 SRX23108231 SRS20063069 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00124   0.00029   0.99853   0.77083   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29781 29781 SRR27435866 SRX23108230 SRS20063066 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep4 EV08007 EV08007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08007.R1.fastq.gz fastq 761961760.0 5442584.0 EV08007.R1.fastq.gz 0:140 A:194053323;C:191169414;G:194452160;T:182234253;N:52610 140       194053323 191169414 194452160 182234253 52610 SRX23108230 SRS20063066 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00242   0.00062   0.99803   0.81818   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
36422 36422 SRR516548 SRX156334 SRS347202 SRP013950 PRJNA169500 Danio rerio embryonic promoterome PRJNA169500 Transcriptome Analysis Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.   pubmed:24531765 Zebrafish wild type AB strain embryo 64 cells stage D. rerio 64 cells embryo D. rerio 64 cells embryo                     CAGE D. rerio 64 cells embryo CAGE D. rerio 64 cells embryo D. rerio 64 cells embryo 1     OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>27</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP013950     CAGE_64cells.fastq fastq 162784188.0 6029044.0 CAGE D. rerio 64 cells embryo 0:27 A:41192860;C:36547869;G:46848833;T:38194626;N:0 27       41192860 36547869 46848833 38194626 0 SRX156334 SRS347202 SRA055273 University of Bergen ZEPROME consortium                       B   usable mapping rate illumina early_illumina unknown cage unknown bulk unknown unknown   Unknown 2013-08-31 Cleavage Embryo Embryo Imprecise All anatomical structures
36993 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
40252 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 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 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 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 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 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
43071 43071 SRR7264575 SRX4168722 SRS3380686 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.4;AG01274.4 AG01273.4;AG01274.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HWKVWADXX_JBCZ103_023_R1.fastq.gz fastq 7514617040.0 98876540.0 HWKVWADXX JBCZ103 023 R1.fastq.gz 0:76 A:2401597632;C:1861527917;G:1834777254;T:1415956870;N:757367 76       2401597632 1861527917 1834777254 1415956870 757367 SRX4168722 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43072 43072 SRR7264576 SRX4168721 SRS3380689 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2 Raw multiplex: ribo seq pata AG01409;ribo seq pata AG01410   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|condition:RPF 28nt|replicate group:19|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal                 Raw multiplex: RPF patA WT 64c RPF B1;RPF patA WT 64c RPF B2 AG01409.1;AG01410.1 AG01409.1;AG01410.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     C7MPPANXX_JBDL115_014_R1.fastq.gz fastq 4944760108.0 65062633.0 C7MPPANXX JBDL115 014 R1.fastq.gz 0:76 A:1280812305;C:1385761238;G:1441128504;T:836702863;N:355198 76       1280812305 1385761238 1441128504 836702863 355198 SRX4168721 SRS3380689 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43073 43073 SRR7264577 SRX4168720 SRS3380688 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2 Raw multiplex: ribo seq pata AG01411;ribo seq pata AG01412   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:cyclohex PatA|molecule:RNA|condition:RPF 28nt|replicate group:20|replicate:1;2|barcode:CACA;TCTC|BioSampleModel:Model organism or animal                 Raw multiplex: RPF patA WT 64c PatA RPF B1;RPF patA WT 64c PatA RPF B2 AG01411.1;AG01412.1 AG01411.1;AG01412.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     C7MPPANXX_JBDM116_015_R1.fastq.gz fastq 10995071544.0 144671994.0 C7MPPANXX JBDM116 015 R1.fastq.gz 0:76 A:2850888928;C:3075001734;G:3215965099;T:1852417694;N:798089 76       2850888928 3075001734 3215965099 1852417694 798089 SRX4168720 SRS3380688 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43074 43074 SRR7264578 SRX4168719 SRS3380687 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 AG01426.1;AG01427.1 AG01426.1;AG01427.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     C7MPPANXX_JBDF109_027_R1.fastq.gz fastq 446991948.0 5881473.0 C7MPPANXX JBDF109 027 R1.fastq.gz 0:76 A:146192524;C:109441919;G:103882304;T:87445288;N:29913 76       146192524 109441919 103882304 87445288 29913 SRX4168719 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   1e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43075 43075 SRR7264579 SRX4168718 SRS3380687 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 AG01426.2;AG01427.2 AG01426.2;AG01427.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJC2ADXX_JBDF109_027_R1.fastq.gz fastq 447485492.0 5887967.0 HVJC2ADXX JBDF109 027 R1.fastq.gz 0:76 A:146683880;C:109166579;G:104154702;T:87473352;N:6979 76       146683880 109166579 104154702 87473352 6979 SRX4168718 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0023   0.00034   0.99326   0.57567   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43076 43076 SRR7264580 SRX4168717 SRS3380687 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 AG01426.3;AG01427.3 AG01426.3;AG01427.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJ2TADXX_JBDF109_027_R1.fastq.gz fastq 4740289176.0 62372226.0 HVJ2TADXX JBDF109 027 R1.fastq.gz 0:76 A:1552060471;C:1156267615;G:1104246757;T:927209997;N:504336 76       1552060471 1156267615 1104246757 927209997 504336 SRX4168717 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00235   0.00026   0.99379   0.60051   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43077 43077 SRR7264581 SRX4168716 SRS3380687 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 Raw multiplex: dmsseq pata AG01426;dmsseq pata AG01427   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS|molecule:RNA|selection:pA|condition:DMS|replicate group:21|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c DMS B1;DMS Seq PatA WT 64c DMS B2 AG01426.4;AG01427.4 AG01426.4;AG01427.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HJTYNBCXX_JBDF109_NOBCX_R1.fastq.gz fastq 6776423036.0 89163461.0 HJTYNBCXX JBDF109 NOBCX R1.fastq.gz 0:76 A:2212424663;C:1653496002;G:1573846163;T:1336100302;N:555906 76       2212424663 1653496002 1573846163 1336100302 555906 SRX4168716 SRS3380687 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 3e-05   2e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43078 43078 SRR7264582 SRX4168715 SRS3380683 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 AG01428.1;AG01429.1 AG01428.1;AG01429.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     C7MPPANXX_JBDG110_013_R1.fastq.gz fastq 1593732388.0 20970163.0 C7MPPANXX JBDG110 013 R1.fastq.gz 0:76 A:517196379;C:393268952;G:372639155;T:310521534;N:106368 76       517196379 393268952 372639155 310521534 106368 SRX4168715 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   0.0   0.99997   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43079 43079 SRR7264583 SRX4168714 SRS3380683 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 AG01428.2;AG01429.2 AG01428.2;AG01429.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJC2ADXX_JBDG110_013_R1.fastq.gz fastq 1268326988.0 16688513.0 HVJC2ADXX JBDG110 013 R1.fastq.gz 0:76 A:411772190;C:312434121;G:297408612;T:246654231;N:57834 76       411772190 312434121 297408612 246654231 57834 SRX4168714 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 1e-05   0.0   0.99997   0.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43080 43080 SRR7264584 SRX4168713 SRS3380683 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 AG01428.3;AG01429.3 AG01428.3;AG01429.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJ2TADXX_JBDG110_013_R1.fastq.gz fastq 1149592188.0 15126213.0 HVJ2TADXX JBDG110 013 R1.fastq.gz 0:76 A:373090462;C:283151050;G:269811169;T:223419849;N:119658 76       373090462 283151050 269811169 223419849 119658 SRX4168713 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00222   0.0002   0.99362   0.55643   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43081 43081 SRR7264585 SRX4168712 SRS3380686 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.3;AG01274.3 AG01273.3;AG01274.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJ7NADXX_JBCZ103_023_R1.fastq.gz fastq 882016024.0 11605474.0 HVJ7NADXX JBCZ103 023 R1.fastq.gz 0:76 A:278837606;C:213606139;G:214029888;T:175477675;N:64716 76       278837606 213606139 214029888 175477675 64716 SRX4168712 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 6e-05   4e-05   0.99995   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43082 43082 SRR7264586 SRX4168711 SRS3380686 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.2;AG01274.2 AG01273.2;AG01274.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVK53ADXX_JBCZ103_023_R1.fastq.gz fastq 2614864056.0 34406106.0 HVK53ADXX JBCZ103 023 R1.fastq.gz 0:76 A:832670351;C:647746556;G:639758530;T:494461931;N:226688 76       832670351 647746556 639758530 494461931 226688 SRX4168711 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 5e-05   2e-05   0.99993   0.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43085 43085 SRR7264589 SRX4168708 SRS3380686 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 Raw multiplex: dmsseq AG01273;dmsseq AG01274   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo cyclohex|molecule:RNA|selection:pA|condition:DMS|replicate group:18|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq WT 64c CHX B1;DMS Seq WT 64c CHX B2 AG01273.1;AG01274.1 AG01273.1;AG01274.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HMHGVADXX_JBCZ103_023_R1.fastq.gz fastq 2819768568.0 37102218.0 HMHGVADXX JBCZ103 023 R1.fastq.gz 0:76 A:900945260;C:699348182;G:689446355;T:529699985;N:328786 76       900945260 699348182 689446355 529699985 328786 SRX4168708 SRS3380686 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43091 43091 SRR7264595 SRX4168702 SRS3380683 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 AG01428.5;AG01429.5 AG01428.5;AG01429.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HJTYNBCXX_JBDG110_NOBCX_R1.fastq.gz fastq 8473348224.0 111491424.0 HJTYNBCXX JBDG110 NOBCX R1.fastq.gz 0:76 A:2738474380;C:2086110939;G:1986494866;T:1661471870;N:796169 76       2738474380 2086110939 1986494866 1661471870 796169 SRX4168702 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 3e-05   2e-05   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43092 43092 SRR7264596 SRX4168701 SRS3380683 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 Raw multiplex: dmsseq pata AG01428;dmsseq pata AG01429   strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1;2|barcode:CACA;AGAG|BioSampleModel:Model organism or animal                 Raw multiplex: DMS Seq PatA WT 64c PatA DMS B1;DMS Seq PatA WT 64c PatA DMS B2 AG01428.4;AG01429.4 AG01428.4;AG01429.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     HVJ7NADXX_JBDG110_013_R1.fastq.gz fastq 1317100672.0 17330272.0 HVJ7NADXX JBDG110 013 R1.fastq.gz 0:76 A:424319849;C:318879376;G:308835829;T:264971153;N:94465 76       424319849 318879376 308835829 264971153 94465 SRX4168701 SRS3380683 SRA715414 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 9e-05   5e-05   0.99995   0.2   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-05 Cleavage Embryo Embryo Imprecise All anatomical structures
43103 43103 SRR5893062 SRX3058783 SRS2404532 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c DMScontrol in vitro AG00876.2 AG00876.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG00876.2_R1.fastq.gz fastq 139395856.0 1834156.0 AG00876.2 R1.fastq.gz 0:76 A:37323535;C:39047425;G:34144869;T:28873865;N:6162 76       37323535 39047425 34144869 28873865 6162 SRX3058783 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.00316   0.00094   0.99318   0.54676   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43104 43104 SRR5893063 SRX3058782 SRS2404532 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c DMScontrol in vitro AG00876.1 AG00876.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG00876.1_R1.fastq.gz fastq 23244372.0 305847.0 AG00876.1 R1.fastq.gz 0:76 A:6246268;C:6429695;G:5629550;T:4937550;N:1309 76       6246268 6429695 5629550 4937550 1309 SRX3058782 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.02737   0.00562   0.96288   0.52983   76   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43117 43117 SRR5893084 SRX3058761 SRS2404540 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.1 AG01429.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01429.1_R1.fastq.gz fastq 193152200.0 7929129.0 AG01429.1 R1.fastq.gz 0:24.36 1:0 A:53713978;C:42339303;G:46822608;T:50276290;N:21 24 0     53713978 42339303 46822608 50276290 21 SRX3058761 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69688   0.0423   0.76621   0.51286   37   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43118 43118 SRR5893085 SRX3058760 SRS2404541 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.5 AG01428.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01428.5_R1.fastq.gz fastq 1471415118.0 60775933.0 AG01428.5 R1.fastq.gz 0:24.21 1:0 A:427869397;C:311916291;G:327280051;T:404336571;N:12808 24 0     427869397 311916291 327280051 404336571 12808 SRX3058760 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69068   0.05351   0.76625   0.51244   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43119 43119 SRR5893086 SRX3058759 SRS2404541 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.4 AG01428.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01428.4_R1.fastq.gz fastq 208326774.0 8582890.0 AG01428.4 R1.fastq.gz 0:24.27 1:0 A:60934366;C:43916600;G:46106309;T:57368748;N:751 24 0     60934366 43916600 46106309 57368748 751 SRX3058759 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.68998   0.05396   0.76374   0.51059   17   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43120 43120 SRR5893087 SRX3058758 SRS2404541 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B1 dmsseq pata AG01428   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B1 AG01428.3 AG01428.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01428.3_R1.fastq.gz fastq 201183036.0 8321263.0 AG01428.3 R1.fastq.gz 0:24.18 1:0 A:58823768;C:42490237;G:44567988;T:55298599;N:2444 24 0     58823768 42490237 44567988 55298599 2444 SRX3058758 SRS2404541 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.6871   0.05281   0.76575   0.51538   30   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43121 43121 SRR5893088 SRX3058757 SRS2404540 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.5 AG01429.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01429.5_R1.fastq.gz fastq 1025355643.0 41973110.0 AG01429.5 R1.fastq.gz 0:24.43 1:0 A:286439080;C:223476222;G:247260097;T:268171035;N:9209 24 0     286439080 223476222 247260097 268171035 9209 SRX3058757 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69958   0.04484   0.76558   0.51603   29   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43122 43122 SRR5893089 SRX3058756 SRS2404540 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.4 AG01429.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01429.4_R1.fastq.gz fastq 145578062.0 5944282.0 AG01429.4 R1.fastq.gz 0:24.49 1:0 A:40943195;C:31523692;G:34943324;T:38167309;N:542 24 0     40943195 31523692 34943324 38167309 542 SRX3058756 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.70235   0.04557   0.76341   0.5093   38   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43123 43123 SRR5893090 SRX3058755 SRS2404540 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.3 AG01429.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01429.3_R1.fastq.gz fastq 140022273.0 5737910.0 AG01429.3 R1.fastq.gz 0:24.40 1:0 A:39343164;C:30378209;G:33656711;T:36642421;N:1768 24 0     39343164 30378209 33656711 36642421 1768 SRX3058755 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69621   0.04502   0.764   0.51161   28   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43124 43124 SRR5893091 SRX3058754 SRS2404540 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq PatA WT 64c PatA DMS B2 dmsseq pata AG01429   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS PatA|molecule:RNA|selection:pA|condition:DMS|replicate group:22|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq PatA WT 64c PatA DMS B2 AG01429.2 AG01429.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01429.2_R1.fastq.gz fastq 155400644.0 6350801.0 AG01429.2 R1.fastq.gz 0:24.47 1:0 A:43541418;C:33799983;G:37361242;T:40698001;N:0 24 0     43541418 33799983 37361242 40698001 0 SRX3058754 SRS2404540 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.70153   0.04589   0.76495   0.51164   21   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43127 43127 SRR5893094 SRX3058751 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.1 AG01042.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.1_R1.fastq.gz fastq 126429566.0 5343149.0 AG01042.1 R1.fastq.gz 0:23.66 1:0 A:33794193;C:29213503;G:32293032;T:31128226;N:612 23 0     33794193 29213503 32293032 31128226 612 SRX3058751 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.60436   0.07589   0.78179   0.58081   23   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43128 43128 SRR5893095 SRX3058750 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.2 AG01042.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.2_R1.fastq.gz fastq 43162881.0 1835075.0 AG01042.2 R1.fastq.gz 0:23.52 1:0 A:11533531;C:9954515;G:11073245;T:10599502;N:2088 23 0     11533531 9954515 11073245 10599502 2088 SRX3058750 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58191   0.07361   0.78255   0.5884   27   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43129 43129 SRR5893096 SRX3058749 SRS2404532 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c DMScontrol in vitro AG00876.3 AG00876.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG00876.3_R1.fastq.gz fastq 981554972.0 12915197.0 AG00876.3 R1.fastq.gz 0:76 A:261237433;C:277515571;G:240090014;T:202665429;N:46525 76       261237433 277515571 240090014 202665429 46525 SRX3058749 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 2e-05   0.0   0.99995   1.0   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43130 43130 SRR5893097 SRX3058748 SRS2404532 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c DMScontrol in vitro dmsseq AG00876   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:water in vitro|molecule:RNA|selection:pA|condition:control|replicate group:13|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c DMScontrol in vitro AG00876.4 AG00876.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG00876.4_R1.fastq.gz fastq 662935688.0 8722838.0 AG00876.4 R1.fastq.gz 0:76 A:176751346;C:187148186;G:162147575;T:136873146;N:15435 76       176751346 187148186 162147575 136873146 15435 SRX3058748 SRS2404532 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.0   0.0   1.0       76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43131 43131 SRR5893098 SRX3058747 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.5 AG01042.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.5_R1.fastq.gz fastq 1080031154.0 45488589.0 AG01042.5 R1.fastq.gz 0:23.74 1:0 A:290744683;C:247189003;G:273714462;T:268297982;N:85024 23 0     290744683 247189003 273714462 268297982 85024 SRX3058747 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.60791   0.07492   0.77979   0.58326   29   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43132 43132 SRR5893099 SRX3058746 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.6 AG01042.6 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.6_R1.fastq.gz fastq 283394970.0 12033965.0 AG01042.6 R1.fastq.gz 0:23.55 1:0 A:76195456;C:65114236;G:72044677;T:70039067;N:1534 23 0     76195456 65114236 72044677 70039067 1534 SRX3058746 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.59876   0.07667   0.78135   0.58397   33   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43133 43133 SRR5893100 SRX3058745 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.3 AG01042.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.3_R1.fastq.gz fastq 635217690.0 26879456.0 AG01042.3 R1.fastq.gz 0:23.63 1:0 A:169915710;C:146718321;G:161940079;T:156641690;N:1890 23 0     169915710 146718321 161940079 156641690 1890 SRX3058745 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.60186   0.07604   0.78186   0.58928   29   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43134 43134 SRR5893101 SRX3058744 SRS2404542 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01042   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:1|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01042.4 AG01042.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01042.4_R1.fastq.gz fastq 737360617.0 31187809.0 AG01042.4 R1.fastq.gz 0:23.64 1:0 A:197816552;C:169921394;G:187620043;T:181992000;N:10628 23 0     197816552 169921394 187620043 181992000 10628 SRX3058744 SRS2404542 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.60088   0.07706   0.78046   0.547   15   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43137 43137 SRR5893104 SRX3058741 SRS2404544 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01046   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01046.1 AG01046.1 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01046.1_R1.fastq.gz fastq 104571264.0 4565699.0 AG01046.1 R1.fastq.gz 0:22.90 1:0 A:26920338;C:24177052;G:26506298;T:26967196;N:380 22 0     26920338 24177052 26506298 26967196 380 SRX3058741 SRS2404544 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.5641   0.06574   0.78437   0.58268   15   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43138 43138 SRR5893105 SRX3058740 SRS2404544 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01046   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01046.2 AG01046.2 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01046.2_R1.fastq.gz fastq 34508189.0 1516870.0 AG01046.2 R1.fastq.gz 0:22.75 1:0 A:8891670;C:7954125;G:8796911;T:8864593;N:890 22 0     8891670 7954125 8796911 8864593 890 SRX3058740 SRS2404544 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.54153   0.06305   0.7852   0.5792   19   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43139 43139 SRR5893106 SRX3058739 SRS2404544 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01046   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01046.3 AG01046.3 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01046.3_R1.fastq.gz fastq 559711334.0 24457578.0 AG01046.3 R1.fastq.gz 0:22.88 1:0 A:144168923;C:129246711;G:141668875;T:144625154;N:1671 22 0     144168923 129246711 141668875 144625154 1671 SRX3058739 SRS2404544 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.56488   0.06449   0.7838   0.57611   20   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43140 43140 SRR5893107 SRX3058738 SRS2404544 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01046   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01046.4 AG01046.4 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01046.4_R1.fastq.gz fastq 639006387.0 27909373.0 AG01046.4 R1.fastq.gz 0:22.90 1:0 A:165043321;C:147246240;G:161359572;T:165354476;N:2778 22 0     165043321 147246240 161359572 165354476 2778 SRX3058738 SRS2404544 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.56251   0.06604   0.78417   0.57986   18   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43141 43141 SRR5893108 SRX3058737 SRS2404544 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       DMS Seq WT 64c in vivo dmsseq AG01046   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS in vivo|molecule:RNA|selection:pA|condition:DMS|replicate group:14|replicate:2|BioSampleModel:Model organism or animal                 DMS Seq WT 64c in vivo AG01046.5 AG01046.5 RNA     OTHER TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP114782     AG01046.5_R1.fastq.gz fastq 810814539.0 35324852.0 AG01046.5 R1.fastq.gz 0:22.95 1:0 A:209392559;C:186085613;G:205018734;T:210262020;N:55613 22 0     209392559 186085613 205018734 210262020 55613 SRX3058737 SRS2404544 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.57046   0.06498   0.78423   0.5699   22   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures

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