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41 rows where devstage_curation = "Blastula" and tissue_curation_coarse = "Embryo Imprecise"

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experiment.library_selection 5

experiment.platform 4

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Embryo Imprecise · 41 ✖

tissue_curation 1

technology 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 41 ✖
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
9723 9723 ERR3841996 ERX3854558 ERS3556001 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 3 SAMEA5752542 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 6 Sphere 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1439954368.0 18946768.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 6 0:76 A:669362698;C:280496524;G:316727778;T:173353505;N:13863 76       669362698 280496524 316727778 173353505 13863 ERX3854558 ERS3556001 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.26155   0.12068   0.96915   0.45719   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9724 9724 ERR3841995 ERX3854557 ERS3556000 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 2 SAMEA5752541 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 5 Sphere 2 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1592272200.0 20950950.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 5 0:76 A:757507948;C:308394094;G:342142775;T:184211881;N:15502 76       757507948 308394094 342142775 184211881 15502 ERX3854557 ERS3556000 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.22483   0.10923   0.97646   0.49458   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9725 9725 ERR3841994 ERX3854556 ERS3555999 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 1 SAMEA5752540 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 4 Sphere 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1332363676.0 17531101.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 4 0:76 A:529354355;C:299445923;G:318745973;T:184804260;N:13165 76       529354355 299445923 318745973 184804260 13165 ERX3854556 ERS3555999 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.21197   0.0829   0.98196   0.55753   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9752 9752 ERR3489858 ERX3511273 ERS3556001 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 3 SAMEA5752542 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 10 Sphere 3 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     2740392724.0 36057799.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 10 0:76 A:1790452280;C:354001675;G:431182140;T:164697730;N:58899 76       1790452280 354001675 431182140 164697730 58899 ERX3511273 ERS3556001 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.87154   0.5323   0.99793   0.02983   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9753 9753 ERR3489857 ERX3511272 ERS3556001 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 3 SAMEA5752542 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752542|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:5|common name:zebrafish|dev stage:Sphere|sample name:5|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 9 Sphere 3 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     6277242192.0 82595292.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 9 0:76 A:3129446012;C:1311888416;G:1369035262;T:466745503;N:126999 76       3129446012 1311888416 1369035262 466745503 126999 ERX3511272 ERS3556001 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.65637   0.35975   0.9936   0.24734   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9754 9754 ERR3489856 ERX3511271 ERS3556000 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 2 SAMEA5752541 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:424 8 Sphere 2 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     6679993476.0 87894651.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 8 0:76 A:3113787833;C:1255798935;G:1750515950;T:559763997;N:126761 76       3113787833 1255798935 1750515950 559763997 126761 ERX3511271 ERS3556000 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.66287   0.41208   0.99602   0.17083   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9755 9755 ERR3489855 ERX3511270 ERS3556000 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 2 SAMEA5752541 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752541|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:4|common name:zebrafish|dev stage:Sphere|sample name:4|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 7 Sphere 2 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     13238731764.0 174193839.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:424 7 0:76 A:7630016769;C:1835321568;G:2775223283;T:997916159;N:253985 76       7630016769 1835321568 2775223283 997916159 253985 ERX3511270 ERS3556000 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.77269   0.45994   0.99683   0.04249   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9756 9756 ERR3489854 ERX3511269 ERS3555999 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 1 SAMEA5752540 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 6 Sphere 1 LSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 24     3311799332.0 43576307.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 6 0:76 A:1182325939;C:888677953;G:922571204;T:318159754;N:64482 76       1182325939 888677953 922571204 318159754 64482 ERX3511269 ERS3555999 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.57505   0.24459   0.99582   0.43365   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
9757 9757 ERR3489853 ERX3511268 ERS3555999 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Sphere 1 SAMEA5752540 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752540|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:3|common name:zebrafish|dev stage:Sphere|sample name:3|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 22 08 2019 11:57:43:423 5 Sphere 1 SSU None RCP seq   OTHER TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 08 22     7403181508.0 97410283.0 ena RUN Computational Biology Unit 22 08 2019 11:57:43:423 5 0:76 A:4338227974;C:1233250165;G:1372229712;T:459322295;N:151362 76       4338227974 1233250165 1372229712 459322295 151362 ERX3511268 ERS3555999 ERA2100634 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.765   0.44747   0.99515   0.12467   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Blastula Embryo Undetermined Embryo Imprecise
10212 10212 ERR6511331 ERX6138167 ERS7264190 ERP131213 PRJEB46978 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 Other Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28   Zebrafish Nano3P seq of PolyA selected sample biological replicate 1 including 4 hpf RNA Zebrafish PolyA 4 hpf SAMEA9541420 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2023 12 28T01:07:23Z|ENA LAST UPDATE:2023 12 28T01:07:23Z|External Id:SAMEA9541420|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:23Z|INSDC last update:2023 12 28T01:07:23Z|INSDC status:public|Submitter Id:Zebrafish PolyA 4 hpf|common name:zebrafish|sample name:Zebrafish PolyA 4 hpf|scientific name:Danio rerio                 MinION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5 cDNA8523612 Nano3P seq Nano3P seq   OTHER TRANSCRIPTOMIC unspecified SINGLE OXFORD_NANOPORE MinION   ERP131213 MinION sequencing ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 zebrafish_polya_4hpf.tar.gz nanopore 330562220.0 233101.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 17 08 2021 13:09:55:665 5 0:1418.11 A:86572446;C:74232962;G:69203462;T:100553350;N:0 1418       86572446 74232962 69203462 100553350 0 ERX6138167 ERS7264190 ERA5757997 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG) 1 0.0   0.0   1.0       1536   T   long read ont ont full_length poly_a unknown bulk unknown unknown   Spain 2023-12-28 Blastula Embryo Undetermined Embryo Imprecise
10214 10214 ERR6617900 ERX6244443 ERS7291130 ERP131213 PRJEB46978 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore sequencing ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-12-08-2021-14:48:52:906-1159 Other Nano3P seq is a simple and robust method to accurately estimate transcript levels tail lengths and tail nucleotide composition information in full length individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28   PolyA selected dRNA sequenced zebrafish 4hpf RNA Zebrafish 4hpf dRNA SAMEA9568396 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2023 12 28T01:07:30Z|ENA LAST UPDATE:2023 12 28T01:07:30Z|External Id:SAMEA9568396|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2023 12 28T01:07:30Z|INSDC last update:2023 12 28T01:07:30Z|INSDC status:public|Submitter Id:Zebrafish 4hpf dRNA1|common name:zebrafish|sample name:Zebrafish 4hpf dRNA1|scientific name:Danio rerio                 MinION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 dRNA Zebrafish Direct RNA Sequencing Direct RNA Sequencing   RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP131213 MinION sequencing ENA FIRST PUBLIC:2023 12 28|ENA LAST UPDATE:2023 12 28 Zebrafish_4hpf_dRNA.fast5.tar.gz nanopore 772304625.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 03 09 2021 14:33:13:450 1 0:860.25 A:224977035;C:165273397;G:156659356;T:225394837;N:0 860       224977035 165273397 156659356 225394837 0 ERX6244443 ERS7291130 ERA5995143 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG) 1 0.5   0.0   0.99997   1.0   962   T   long read ont ont full_length poly_a unknown bulk unknown unknown   Spain 2023-12-28 Blastula Embryo Undetermined Embryo Imprecise
11045 11045 ERR9839778 ERX9385635 ERS12199235 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish PolyA Selected RNA 4hpf Zebrafish pA selected SAMEA110100410 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100410|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish pA selected|common name:zebrafish|sample name:Zebrafish pA selected                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 811 cDNA852361 ZFPA4R1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA852361_ZFPA4R1.tar.gz nanopore 348224822.0 233101.0 ena RUN TAB 13 06 2022 16:07:52:807 812 0:1493.88 A:88963756;C:76104775;G:73909507;T:109246784;N:0 1493       88963756 76104775 73909507 109246784 0 ERX9385635 ERS12199235 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG) 1 0.34147   0.26829   0.99993   0.16666   1537   T   long read ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Blastula Embryo Undetermined Embryo Imprecise
24548 24548 ERR964669 ERX1041632 ERS792103 ERP011038 PRJEB9889 The Zebrafish transcriptome during early development ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 Other Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.       KI BN JKE DRERIO RNASEQ SAMEA3484818 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   ERP011038 AB SOLiD System 3.0 sequencing ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-512cell_F3_QV.qual.gz SOLiD_native SOLiD_native 5452772750.0 109055455.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 3 0:50 0:1391108289;1:1312099760;2:1551659810;3:1179923010;.:17981881 50                 ERX1041632 ERS792103 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.73133   0.07897   0.88057   0.63645   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Blastula Embryo Undetermined Embryo Imprecise
24552 24552 ERR964673 ERX1041636 ERS792103 ERP011038 PRJEB9889 The Zebrafish transcriptome during early development ena-STUDY-KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION-15-07-2015-15:13:51:747-22 Other Zebrafish has emerged as a model organism to investigate vertebrate development and human genetic diseases. However currently zebrafish annotation is still ongoing and clearly not sufficed therefore providing opportunity for novel transcript finding. With the introduction of massive parallel sequencing whole transcriptome investigations became possible through assembling entire transcriptome from overlapped sequencing reads. In the study we were aiming to discover novel transcribed regions NTRs using data from RNA sequencing. We have developed an in house bioinformatics pipeline for NTR discovery. Using the pipeline we detected 165 putative NTRs which could involve in early zebrafish development and not annotated anywhere. Six randomly selected NTRs were successfully validated experimentally using RT PCR. These NTRs provided new candidates for zebrafish transcriptome studies and zebrafish genome annotation.       KI BN JKE DRERIO RNASEQ SAMEA3484818 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484818|INSDC center alias:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC center name:KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|INSDC first public:2015 07 16T15:54:30Z|INSDC last update:2015 07 15T15:02:15Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2009 512cell|common name:zebrafish|dev stage:512 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 512cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   ERP011038 AB SOLiD System 3.0 sequencing ENA FIRST PUBLIC:2015 07 16|ENA LAST UPDATE:2018 11 16 KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-512cell_F3_QV.qual.gz SOLiD_native SOLiD_native 2027760000.0 40555200.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 7 0:50 0:511413081;1:492642968;2:594959353;3:426692118;.:2052480 50                 ERX1041636 ERS792103 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.77106   0.08154   0.85675   0.64875   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Blastula Embryo Undetermined Embryo Imprecise
36666 36666 SRR800043 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz Illumina native 3029181300.0 60583626.0 7986X2 110510 SN141 0338 AB06MWABXX 7 0:50 A:768949744;C:733340278;G:903149841;T:623482299;N:259138 50       768949744 733340278 903149841 623482299 259138 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.83515   0.15524   0.81209   0.81031   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36667 36667 SRR800044 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz Illumina native 3947123500.0 78942470.0 7986X2 110606 SN141 0359 BD0D8KABXX 6 0:50 A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861 50       1000468440 957437794 1171831772 817292633 92861 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.81283   0.14906   0.81335   0.81698   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
37185 37185 SRR1010334 SRX363385 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_transgene_R1.fastq MUTL7F_transgene_R2.fastq fastq fastq 30678849.0 444621.0 D. rerio MUTL7F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:5994534;C:7452275;G:9596502;T:7623459;N:12079 34 35     5994534 7452275 9596502 7623459 12079 SRX363385 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.38487 0.37445 0.0013 9e-05 0.99841 0.99991 0.00309 0.00012 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37186 37186 SRR1010333 SRX363384 SRS490049 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL7F transgenic line   strain:AB strain MUTL7F line|development stage:high 3.3 hpf                 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL7F_endogenous_R2.fastq MUTL7F_endogenous_R1.fastq fastq fastq 78367233.0 1135757.0 D. rerio MUTL7F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:21010895;C:20506800;G:21883789;T:14935556;N:30193 34 35     21010895 20506800 21883789 14935556 30193 SRX363384 SRS490049 SRA104816 University of Bergen ZEPROME consortium 2 0.56643 0.02972 6e-05 0.00056 0.99965 0.99995 0.00017 0.05769 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37187 37187 SRR1010332 SRX363383 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_transgene_R2.fastq MUTL6F_transgene_R1.fastq fastq fastq 36838272.0 533888.0 D. rerio MUTL6F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:7267891;C:8939911;G:11513757;T:9101861;N:14852 34 35     7267891 8939911 11513757 9101861 14852 SRX363383 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.35237 0.20738 0.00196 4e-05 0.9991 0.99987 0.00131 0.00022 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37188 37188 SRR1010331 SRX363382 SRS490048 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL6F transgenic line   strain:AB strain MUTL6F line|development stage:high 3.3 hpf                 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL6F_endogenous_R1.fastq MUTL6F_endogenous_R2.fastq fastq fastq 67887582.0 983878.0 D. rerio MUTL6F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:18224546;C:17687428;G:19119778;T:12829091;N:26739 34 35     18224546 17687428 19119778 12829091 26739 SRX363382 SRS490048 SRA104816 University of Bergen ZEPROME consortium 2 0.57761 0.02201 0.0001 0.00048 0.99975 0.99991 0.00011 0.02247 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37189 37189 SRR1010330 SRX363381 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_transgene_R1.fastq MUTL5F_transgene_R2.fastq fastq fastq 48750708.0 706532.0 D. rerio MUTL5F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:9468865;C:11866504;G:15193605;T:12203213;N:18521 34 35     9468865 11866504 15193605 12203213 18521 SRX363381 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.37677 0.39423 0.0018 0.00013 0.99801 0.99989 0.00295 0.00011 34 35 B B biological fallback assumption illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37190 37190 SRR1010329 SRX363380 SRS490047 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL5F transgenic line   strain:AB strain MUTL5F line|development stage:high 3.3 hpf                 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL5F_endogenous_R1.fastq MUTL5F_endogenous_R2.fastq fastq fastq 85325883.0 1236607.0 D. rerio MUTL5F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22831000;C:22316529;G:23804395;T:16340044;N:33915 34 35     22831000 22316529 23804395 16340044 33915 SRX363380 SRS490047 SRA104816 University of Bergen ZEPROME consortium 2 0.59785 0.01902 0.00632 0.00081 0.99941 0.99993 0.00056 0.11235 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37191 37191 SRR1010328 SRX363379 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_transgene_R1.fastq MUTL2F_transgene_R2.fastq fastq fastq 68247900.0 989100.0 D. rerio MUTL2F transgenic line single locus CAGE mutated sf3a2:mCherry transgene 0:34 1:35 A:13037092;C:16853304;G:21557175;T:16772703;N:27626 34 35     13037092 16853304 21557175 16772703 27626 SRX363379 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.37746 0.14836 0.00135 0.00215 0.99912 0.99995 0.00128 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37192 37192 SRR1010327 SRX363378 SRS490046 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with mutated sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio MUTL2F transgenic line   strain:AB strain MUTL2F line|development stage:high 3.3 hpf                 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     MUTL2F_endogenous_R1.fastq MUTL2F_endogenous_R2.fastq fastq fastq 85300215.0 1236235.0 D. rerio MUTL2F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:22860161;C:22364533;G:24027064;T:16015109;N:33348 34 35     22860161 22364533 24027064 16015109 33348 SRX363378 SRS490046 SRA104816 University of Bergen ZEPROME consortium 2 0.57324 0.0117 0.01138 0.00049 0.99943 0.99993 0.00087 0.02941 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37193 37193 SRR1010326 SRX363377 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_transgene_R1.fastq WTL3F_transgene_R2.fastq fastq fastq 36051879.0 522491.0 D. rerio WTL3F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:6990071;C:8680451;G:10883119;T:9484027;N:14211 34 35     6990071 8680451 10883119 9484027 14211 SRX363377 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.43354 0.14606 0.00247 9e-05 0.99896 0.99991 0.00217 0.00032 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37194 37194 SRR1010325 SRX363376 SRS490045 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL3F transgenic line   strain:AB strain WTL3F line|development stage:high 3.3 hpf                 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL3F_endogenous_R1.fastq WTL3F_endogenous_R2.fastq fastq fastq 78469284.0 1137236.0 D. rerio WTL3F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:21059562;C:20597989;G:21976657;T:14804744;N:30332 34 35     21059562 20597989 21976657 14804744 30332 SRX363376 SRS490045 SRA104816 University of Bergen ZEPROME consortium 2 0.54772 0.02239 3e-05 0.0 0.99979 0.99993 0.00012 0.06756 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37195 37195 SRR1010324 SRX363375 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_transgene_R1.fastq WTL2F_transgene_R2.fastq fastq fastq 67052544.0 971776.0 D. rerio WTL2F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:12413417;C:16491074;G:20506887;T:17614500;N:26666 34 35     12413417 16491074 20506887 17614500 26666 SRX363375 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.47234 0.16966 0.00033 0.00039 0.99918 0.99993 0.00051 0.0 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37196 37196 SRR1010323 SRX363374 SRS490044 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL2F transgenic line   strain:AB strain WTL2F line|development stage:high 3.3 hpf                 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL2F_endogenous_R1.fastq WTL2F_endogenous_R2.fastq fastq fastq 71493591.0 1036139.0 D. rerio WTL2F transgenic line single locus CAGE endogenous sf3a2 0:34 1:35 A:19123161;C:18705556;G:20092193;T:13545180;N:27501 34 35     19123161 18705556 20092193 13545180 27501 SRX363374 SRS490044 SRA104816 University of Bergen ZEPROME consortium 2 0.56581 0.02161 0.00279 0.00056 0.99949 0.99991 0.00025 0.09333 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37197 37197 SRR1010322 SRX363361 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_transgene_R1.fastq WTL1F_transgene_R2.fastq fastq fastq 95222070.0 1380030.0 D. rerio WTL1F transgenic line single locus CAGE wild type sf3a2:mCherry transgene 0:34 1:35 A:17371572;C:23537350;G:29495884;T:24779827;N:37437 34 35     17371572 23537350 29495884 24779827 37437 SRX363361 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.44573 0.30978 0.00036 0.00019 0.99943 0.99991 0.00023 0.00124 34 35 B B mate2-mate1 similar by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
37198 37198 SRR1010321 SRX363360 SRS490033 SRP030770 PRJNA222234 Danio rerio Targeted Locus Loci PRJNA222234 Transcriptome Analysis Goal of this study is to functionally validate regulatory elements within sf3a2 gene promoter which guide transcription start site selection for that promoter in the zebrafish oocyte.   pubmed:24531765 stable transgenic line with wild type sf3a2 promoter construct driving expression of mCherry Generic sample from Danio rerio D. rerio WTL1F transgenic line   strain:AB strain WTL1F line|dev stage:high 3.3 hpf                 D. rerio WTL1F transgenic line single locus CAGE endogenous sf3a2 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 1 1     OTHER TRANSCRIPTOMIC CAGE PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>69</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>35</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP030770     WTL1F_endogenous_R1.fastq WTL1F_endogenous_R2.fastq fastq fastq 64955082.0 941378.0 D. rerio WTL1F transgenic line single locus CAGE endogeneous sf3a2 0:34 1:35 A:17404375;C:16997013;G:18318738;T:12210960;N:23996 34 35     17404375 16997013 18318738 12210960 23996 SRX363360 SRS490033 SRA104816 University of Bergen ZEPROME consortium 2 0.55528 0.02138 9e-05 0.00135 0.99963 0.99991 9e-05 0.10169 34 35 B T mate2 technical by mapping diff illumina hiseq_era unknown cage unknown bulk unknown unknown   Unknown 2014-02-10 Blastula Embryo Undetermined Embryo Imprecise
50622 50622 SRR8182170 SRX5002137 SRS4036800 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 4hpf RNA seq rep2 GSM3467120   tissue:Soma 4hpf RNA seq replicate 2|cell type:somatic cells|developmental stage:4hpf Soma 4hpf RNA seq rep2 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. Soma 4hpf RNA seq replicate 2   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:4hpf GSM3467120 GSM3467120: Soma 4hpf RNA seq rep2; Danio rerio; RNA Seq GSM3467120   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467120 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_4h_rep2_R1.fastq.gz Soma_4h_rep2_R2.fastq.gz fastq fastq 10173597286.0 50364343.0 GSM3467120 r1 0:101 1:101 A:1758957774;C:3313098011;G:3340445531;T:1760473492;N:622478 101 101     1758957774 3313098011 3340445531 1760473492 622478 SRX5002137 SRS4036800 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.98006 0.98041 0.2339 0.21385 0.87807 0.87969 0.88841 0.91714 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Blastula Embryo Undetermined Embryo Imprecise
50623 50623 SRR8182169 SRX5002136 SRS4036799 SRP168473 PRJNA505329 Retention of paternal epigenetic memory in the developing teleost germline [RNA Seq] GSE122480 Transcriptome Analysis Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell PGC formation. However it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage specificity and that are uncoupled from DNA methylation mediated regulation. Overall design: Using low input RNA seq we have profiled transcriptomes of zebrafish primordial germ cells PGCs and age matched somatic cells at 4 blastula 7 gastrula 24 pharyngula prim 5 and 36 pharyngula prim 25 hpf parent bioproject:PRJNA506076 pubmed:31296860   Soma 4hpf RNA seq rep1 GSM3467119   tissue:Soma 4hpf RNA seq replicate 1|cell type:somatic cells|developmental stage:4hpf Soma 4hpf RNA seq rep1 Adaptor sequences and low quality bases were removed using TrimGalore https://github.com/FelixKrueger/TrimGalore/ Sequencing reads were aligned to zebrafish genome danRer10 using STAR Dobin et al 2013; Bioinformatics Transcript abundancies were quantified using RSEM tool Li et al 2011 BMC Bioinformatics Differential gene expression analysis was performed using edgeR Robinson et al 2010; Bioinformatics; McCarthy et al 2012; Nucleic Acids Research Genome build: danRer10 Supplementary files format and content: .csv format containing transcripts per million TPM; expected count and effective length for PGCs and Soma RNA seq samples at 4 developmental stages in replicates. Soma 4hpf RNA seq replicate 1   PGCs were FACS sorted from the kop EGFP F nos3’UTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp   cell type:somatic cells|developmental stage:4hpf GSM3467119 GSM3467119: Soma 4hpf RNA seq rep1; Danio rerio; RNA Seq GSM3467119   1 PGCs were FACS sorted from the kop EGFP F nosthree primeUTR transgenic zebrafish line Library prep was performed using Clontech SMARTer pico mammalian v2 kit and sequenced on NovaSeq 6000 2x100bp GEO Accession:GSM3467119 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP168473     Soma_4h_rep1_R1.fastq.gz Soma_4h_rep1_R2.fastq.gz fastq fastq 9930457966.0 49160683.0 GSM3467119 r1 0:101 1:101 A:1698081743;C:3265573991;G:3282791612;T:1683403802;N:606818 101 101     1698081743 3265573991 3282791612 1683403802 606818 SRX5002136 SRS4036799 SRA808716 GEO Developmental Epigenomics, Genomics and Epigenetics, Garvan Institute 2 0.97789 0.97905 0.22996 0.20755 0.89325 0.89321 0.90876 0.93428 101 101 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Australia 2018-11-13 Blastula Embryo Undetermined Embryo Imprecise
59497 59497 SRR11924327 SRX8469999 SRS6770650 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA oblong 2 GSM4591066   source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA oblong 2 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. oblong   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591066 GSM4591066: small RNA oblong 2; Danio rerio; OTHER GSM4591066   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591066 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_oblong_stage_2.fastq fastq 131762340.0 2740821.0 GSM4591066 r1 0:48.07 A:36963883;C:35740715;G:33446415;T:25611327;N:0 48       36963883 35740715 33446415 25611327 0 SRX8469999 SRS6770650 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.5346   0.11052   0.8967   0.64134   72   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
59498 59498 SRR11924326 SRX8469998 SRS6770649 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA oblong 1 GSM4591065   source name:oblong|tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA oblong 1 Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. oblong   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:oblong|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591065 GSM4591065: small RNA oblong 1; Danio rerio; OTHER GSM4591065   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591065 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_oblong_stage_1.fastq fastq 90701340.0 2141489.0 GSM4591065 r1 0:42.35 A:25203959;C:24291162;G:23143516;T:18062703;N:0 42       25203959 24291162 23143516 18062703 0 SRX8469998 SRS6770649 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.48132   0.15952   0.8756   0.56134   29   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
59500 59500 SRR11924324 SRX8469996 SRS6770647 SRP265951 PRJNA637293 The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites GSE151797 Other A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates except for adult tail trunk that was in duplicate.   pubmed:32912962   small RNA 15E GSM4591063   source name:zfs:0000015|tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt small RNA 15E Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence. zfs:0000015   Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System.   tissue:zfs:0000015|rna fraction:whole cell RNA depleted for rRNA and size selected for RNA < 200 nt GSM4591063 GSM4591063: small RNA 15E; Danio rerio; OTHER GSM4591063   1 Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. For small RNA library construction one ug of whole cell RNA was subjected to rRNA depletion using the RiboMinusT Eukaryote System v2 Invitrogen and small RNA libraries were constructed using Ion Total RNA Seq Kit v2 ThermoFisher Scientific with minor modifications. In short the rRNA depleted RNA samples were enriched for small RNA <200 nt using the magnetic bead clean up module supplied with the kit or MonarchR RNA Cleanup Kit New England Biolabs adapters diluted 1:2 were ligated to the RNA for 2 h and the RNA subsequently reverse transcribed using Superscript IV ThermoFisher Scientific. The cDNA was purified using the magnetic bead clean up module without xxx selection. Amplification of cDNA and purification was performed according to the manufacturer. Manual template preparation of libraries was carried out on the Ion OneTouchTM 2 System ThermoFisher Scientific and sequenced on Ion 540TM chips the Ion GeneStudio S5 System. GEO Accession:GSM4591063 OTHER TRANSCRIPTOMIC other SINGLE ION_TORRENT Ion Torrent S5   SRP265951     small_RNA_15E_stage.fastq fastq 264453879.0 5777826.0 GSM4591063 r1 0:45.77 A:63859672;C:67381369;G:71681258;T:61531580;N:0 45       63859672 67381369 71681258 61531580 0 SRX8469996 SRS6770647 SRA1083099 GEO RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen 1 0.60375   0.23463   0.87606   0.58681   40   B   usable mapping rate ion_torrent ion_torrent unknown rrna_depletion unknown bulk unknown unknown   Denmark 2020-06-04 Blastula Embryo Undetermined Embryo Imprecise
65978 65978 SRR24807860 SRX20580021 SRS17881936 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   RNAseq rnaseh1MO GSM7444958   source name:dome|tissue:dome|genotype:Wild type|treatment:rnaseh1 MO injection RNAseq rnaseh1MO Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 danRer7 Tab delimited text files include features' raw counts for each sample dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:rnaseh1 MO injection GSM7444958 GSM7444958: RNAseq rnaseh1MO; Danio rerio; RNA Seq GSM7444958   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM7444958 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py RNAseq_rnaseh1MO_R1.fastq.gz RNAseq_rnaseh1MO_R2.fastq.gz fastq fastq 12377372100.0 41257907.0 GSM7444958 r1 0:150 1:150 A:3525844584;C:2671948548;G:2742000835;T:3437433380;N:144753 150 150     3525844584 2671948548 2742000835 3437433380 144753 SRX20580021 SRS17881936 SRA1289147 GEO Tsinghua University 2 0.93919 0.93965 0.09234 0.09273 0.73233 0.73229 0.49442 0.49124 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-06-02 Blastula Embryo Undetermined Embryo Imprecise
65979 65979 SRR24807859 SRX20580020 SRS17881935 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   RNAseq StdMO GSM7444957   source name:dome|tissue:dome|genotype:Wild type|treatment:Std MO injection RNAseq StdMO Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 danRer7 Tab delimited text files include features' raw counts for each sample dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:Std MO injection GSM7444957 GSM7444957: RNAseq StdMO; Danio rerio; RNA Seq GSM7444957   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM7444957 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py RNAseq_StdMO_R1.fastq.gz RNAseq_StdMO_R2.fastq.gz fastq fastq 12356028600.0 41186762.0 GSM7444957 r1 0:150 1:150 A:3554019122;C:2636380806;G:2705589158;T:3459897306;N:142208 150 150     3554019122 2636380806 2705589158 3459897306 142208 SRX20580020 SRS17881935 SRA1289147 GEO Tsinghua University 2 0.94213 0.94261 0.09919 0.09907 0.74006 0.74085 0.509 0.50989 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2023-06-02 Blastula Embryo Undetermined Embryo Imprecise
65980 65980 SRR19264694 SRX15325095 SRS13103755 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   Zebrafish hRNaseH1 dome RNA seq Rep2 GSM6165457   source name:dome|tissue:dome|genotype:Wild type|treatment:hRNaseH1 injection Zebrafish hRNaseH1 dome RNA seq Rep2 Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 Assembly: danRer7 Supplementary files format and content: bw dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:hRNaseH1 injection GSM6165457 GSM6165457: Zebrafish hRNaseH1 dome RNA seq Rep2; Danio rerio; RNA Seq GSM6165457   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM6165457 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py hRNaseH1-dome_RNA-seq_Rep2_1.fq.gz hRNaseH1-dome_RNA-seq_Rep2_2.fq.gz fastq fastq 6646729800.0 22155766.0 GSM6165457 r1 0:150 1:150 A:1741981818;C:1583067402;G:1589966949;T:1731612285;N:101346 150 150     1741981818 1583067402 1589966949 1731612285 101346 SRX15325095 SRS13103755 SRA1289147 GEO Tsinghua University 2 0.95539 0.95454 0.03703 0.03697 0.7529 0.75315 0.48127 0.48248 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2022-05-18 Blastula Embryo Undetermined Embryo Imprecise
65981 65981 SRR19264693 SRX15325094 SRS13103754 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   Zebrafish hRNaseH1 dome RNA seq Rep1 GSM6165456   source name:dome|tissue:dome|genotype:Wild type|treatment:hRNaseH1 injection Zebrafish hRNaseH1 dome RNA seq Rep1 Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 Assembly: danRer7 Supplementary files format and content: bw dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:hRNaseH1 injection GSM6165456 GSM6165456: Zebrafish hRNaseH1 dome RNA seq Rep1; Danio rerio; RNA Seq GSM6165456   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM6165456 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py hRNaseH1-dome_RNA-seq_Rep1_1.fq.gz hRNaseH1-dome_RNA-seq_Rep1_2.fq.gz fastq fastq 6806380200.0 22687934.0 GSM6165456 r1 0:150 1:150 A:1785002966;C:1620619662;G:1624295599;T:1776432628;N:29345 150 150     1785002966 1620619662 1624295599 1776432628 29345 SRX15325094 SRS13103754 SRA1289147 GEO Tsinghua University 2 0.95539 0.95483 0.03708 0.03669 0.75519 0.75404 0.48254 0.47527 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2022-05-18 Blastula Embryo Undetermined Embryo Imprecise
65982 65982 SRR19264692 SRX15325093 SRS13103753 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   Zebrafish GFP dome RNA seq Rep2 GSM6165455   source name:dome|tissue:dome|genotype:Wild type|treatment:GFP injection Zebrafish GFP dome RNA seq Rep2 Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 Assembly: danRer7 Supplementary files format and content: bw dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:GFP injection GSM6165455 GSM6165455: Zebrafish GFP dome RNA seq Rep2; Danio rerio; RNA Seq GSM6165455   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM6165455 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py GFP-dome_RNA-seq_Rep2_1.fq.gz GFP-dome_RNA-seq_Rep2_2.fq.gz fastq fastq 6859600500.0 22865335.0 GSM6165455 r1 0:150 1:150 A:1806433143;C:1625894099;G:1633785646;T:1793381963;N:105649 150 150     1806433143 1625894099 1633785646 1793381963 105649 SRX15325093 SRS13103753 SRA1289147 GEO Tsinghua University 2 0.95316 0.95195 0.05856 0.0584 0.74686 0.74704 0.4944 0.49521 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2022-05-18 Blastula Embryo Undetermined Embryo Imprecise
65983 65983 SRR19264691 SRX15325092 SRS13103752 SRP335733 PRJNA760904 R loop landscapes during parental to zygotic transition in zebrafish GSE183453 Other The R loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here we developed a novel R loop profiling technique ULI ssDRIP seq to decte global R loops from a limited number of cells. Based on this method we profiled the R loop landscapes during parental to zygotic transition and early development regulatory in zebrafish and revealed a series of important characters of R loops. Overall design: ULI ssDRIP seq development and R loop profiling in zebrafish   pubmed:38974143   Zebrafish GFP dome RNA seq Rep1 GSM6165454   source name:dome|tissue:dome|genotype:Wild type|treatment:GFP injection Zebrafish GFP dome RNA seq Rep1 Basecalls were performed using bcl2fastq v2.17 for Novaseq output. Sequence reads were trimmed for adaptor sequence/low quality sequence using TrimGalore version 0.6.7. Trimmed sequence reads were mapped to danRer7 using HISTAT2 version 2.2.1 with default parameters. Raw counts for the feature of genes were extracted by featureCounts version 2.0.3. BigWig files were generated by using deepTools version 2.4.2 Assembly: danRer7 Supplementary files format and content: bw dome   Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations.   tissue:dome|genotype:Wild type|treatment:GFP injection GSM6165454 GSM6165454: Zebrafish GFP dome RNA seq Rep1; Danio rerio; RNA Seq GSM6165454   1 Total RNA was extracted by TRIzol method and integrity was assessed using the Fragment Analyzer 5400. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer' s recommendations. GEO Accession:GSM6165454 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP335733   loader:fastq load.py GFP-dome_RNA-seq_Rep1_1.fq.gz GFP-dome_RNA-seq_Rep1_2.fq.gz fastq fastq 6852929700.0 22843099.0 GSM6165454 r1 0:150 1:150 A:1807624022;C:1621249807;G:1628581234;T:1795363171;N:111466 150 150     1807624022 1621249807 1628581234 1795363171 111466 SRX15325092 SRS13103752 SRA1289147 GEO Tsinghua University 2 0.95097 0.95068 0.06105 0.0608 0.74485 0.74464 0.48655 0.49028 150 150 B B biological fallback assumption illumina novaseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2022-05-18 Blastula Embryo Undetermined Embryo Imprecise

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