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67 rows where experiment.library_layout = "SINGLE", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Embryo Imprecise"

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experiment.library_selection 4

experiment.platform 3

tissue_curation_coarse 1

  • Embryo Imprecise · 67 ✖

tissue_curation 1

technology 1

experiment.library_strategy 1

  • RNA-Seq · 67 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 67 ✖

devstage_curation_coarse 1

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
9719 9719 ERR3842000 ERX3854562 ERS4268611 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Shield 4Ei SAMEA6504165 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:05:06Z|ENA LAST UPDATE:2020 01 27T16:04:35Z|External Id:SAMEA6504165|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:05:06Z|INSDC last update:2020 01 27T16:04:35Z|INSDC status:public|Submitter Id:Shield 4Ei|common name:zebrafish|sample name:Shield 4Ei|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 10 Shield 4Ei OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1435748376.0 18891426.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 10 0:76 A:489056518;C:372290023;G:393663734;T:180723629;N:14472 76       489056518 372290023 393663734 180723629 14472 ERX3854562 ERS4268611 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.11942   0.03394   0.98971   0.62271   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9720 9720 ERR3841999 ERX3854561 ERS3556006 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Shield 3 SAMEA5752547 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752547|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:10|common name:zebrafish|dev stage:Shield|sample name:10|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 9 Shield 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1168482976.0 15374776.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 9 0:76 A:516070340;C:238363428;G:268806793;T:145231087;N:11328 76       516070340 238363428 268806793 145231087 11328 ERX3854561 ERS3556006 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.22586   0.10275   0.97281   0.47683   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9721 9721 ERR3841998 ERX3854560 ERS3556007 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Shield 4150NT SAMEA5752548 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752548|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:11|common name:zebrafish|dev stage:Shield|sample name:11|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 8 Shield 150NT OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1188343980.0 15636105.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 8 0:76 A:580658556;C:223116826;G:260847322;T:123709681;N:11595 76       580658556 223116826 260847322 123709681 11595 ERX3854560 ERS3556007 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.27037   0.13972   0.97392   0.39459   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9722 9722 ERR3841997 ERX3854559 ERS3556004 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     Shield 1 SAMEA5752545 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752545|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:8|common name:zebrafish|dev stage:Shield|sample name:8|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 7 Shield 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1278891444.0 16827519.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 7 0:76 A:571738369;C:256385478;G:295145281;T:155610082;N:12234 76       571738369 256385478 295145281 155610082 12234 ERX3854559 ERS3556004 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.23116   0.11137   0.97932   0.45978   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Gastrula Embryo Undetermined Embryo Imprecise
9723 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
9726 9726 ERR3841993 ERX3854555 ERS3555998 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 2 SAMEA5752539 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752539|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:2|common name:zebrafish|dev stage:64 cell|sample name:2|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 3 64 cell 3 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1579307816.0 20780366.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 3 0:76 A:589876602;C:380048242;G:392473318;T:216893826;N:15828 76       589876602 380048242 392473318 216893826 15828 ERX3854555 ERS3555998 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.15411   0.04564   0.97883   0.55376   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9727 9727 ERR3841992 ERX3854554 ERS3556003 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 4Ei 10 SAMEA5752544 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752544|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:7|common name:zebrafish|dev stage:64 cell|sample name:7|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:406 2 64 cell 4Ei OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1213585480.0 15968230.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 2 0:76 A:548456563;C:244465528;G:271963808;T:148687764;N:11817 76       548456563 244465528 271963808 148687764 11817 ERX3854554 ERS3556003 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.21973   0.10926   0.97419   0.44348   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9728 9728 ERR3841991 ERX3854553 ERS3555997 ERP116106 PRJEB33323 Deconstructing the individual steps of vertebrate translation initiation ena-STUDY-Computational Biology Unit-03-07-2019-10:11:34:314-422 Other In eukaryotes the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA their success in navigating its five prime untranslated region UTR and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1 but despite this centrality it remains poorly understood 2 3. Here we introduce ribosome complex profiling RCP seq to capture the transcriptome wide occupancy of scanning initiating elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all five prime UTRs in zebrafish which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment scanning of the five prime UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the five prime UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate. ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2019 07 03     64 cell 1 SAMEA5752538 Computational Biology Unit ENA FIRST PUBLIC:2020 03 27T17:04:59Z|ENA LAST UPDATE:2019 07 03T10:01:14Z|External Id:SAMEA5752538|INSDC center name:Computational Biology Unit|INSDC first public:2020 03 27T17:04:59Z|INSDC last update:2019 07 03T10:01:14Z|INSDC status:public|Submitter Id:1|common name:zebrafish|dev stage:64 cell|sample name:1|scientific name:Danio rerio                 NextSeq 500 sequencing ena EXPERIMENT Computational Biology Unit 27 01 2020 16:24:36:405 1 64 cell 1 OTHER RNA Seq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA NextSeq 500   ERP116106 NextSeq 500 sequencing ENA FIRST PUBLIC:2020 03 27|ENA LAST UPDATE:2020 02 14     1494930944.0 19670144.0 ena RUN Computational Biology Unit 27 01 2020 16:24:36:406 1 0:76 A:543017836;C:366974203;G:367027373;T:217896401;N:15131 76       543017836 366974203 367027373 217896401 15131 ERX3854553 ERS3555997 ERA2359305 Computational Biology Unit|European Nucleotide Archive Computational Biology Unit 1 0.2544   0.08957   0.96568   0.55681   76   B   usable mapping rate illumina nextseq unknown other unknown bulk unknown unknown   Unknown 2019-07-03 Cleavage Embryo Undetermined Embryo Imprecise
9919 9919 ERR5167510 ERX4972431 ERS5593364 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     cDNA WT 2hpf rep1 JD T20 PDPN191089   ENA FIRST PUBLIC:2022 07 05T12:06:34Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:34Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05         ena RUN CENTER FOR GENOMIC REGULATION CRG 21 01 2021 22:16:50:154 1                       ERX4972431   ERA3319053 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Cleavage Embryo Undetermined Embryo Imprecise
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
11042 11042 ERR9839781 ERX9385638 ERS12199238 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep3 SAMEA110100413 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100413|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep3|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep3                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 817 cDNA897892 ZFRDR3 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA897892_ZFRDR3.tar.gz nanopore 848659575.0 587586.0 ena RUN TAB 13 06 2022 16:07:52:808 818 0:1444.32 A:210205014;C:186527780;G:188214279;T:263712502;N:0 1444       210205014 186527780 188214279 263712502 0 ERX9385638 ERS12199238 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11043 11043 ERR9839780 ERX9385637 ERS12199237 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep2 SAMEA110100412 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100412|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep2|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep2                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 815 cDNA123791 ZFRDR2 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA123791_ZFRDR2.tar.gz nanopore 2229275175.0 1955617.0 ena RUN TAB 13 06 2022 16:07:52:807 816 0:1139.93 A:533543922;C:498938137;G:515833119;T:680959997;N:0 1139       533543922 498938137 515833119 680959997 0 ERX9385637 ERS12199237 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11044 11044 ERR9839779 ERX9385636 ERS12199236 ERP138294 PRJEB53494 Nano3P seq: transcriptome wide analysis of gene expression and tail dynamics using end capture nanopore cDNA sequencing 94bf5509-4622-4d5f-b7c5-6a14bdfac340 Other RNA polyadenylation plays a central role in RNA maturation fate and stability. In response to developmental cues polyA tail lengths can vary affecting the translation efficiency and stability of mRNAs. Here we develop Nanopore three prime end capture sequencing Nano3P seq a novel method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance tail composition and tail length dynamics at per read resolution. By employing a template switching based sequencing protocol Nano3P seq can sequence any given RNA molecule from its three prime end regardless of its polyadenylation status without xxx need for PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P seq captures a wide diversity of RNA biotypes providing quantitative estimates of RNA abundance and tail lengths in mRNA lncRNA sn/snoRNA scaRNA and rRNA molecules. We find that in addition to mRNA and lncRNA polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish models. Moreover we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at an isoform specific level correlating with mRNA decay. Finally we identify non A bases within polyA tails of various lengths and reveal their distribution during vertebrate embryogenesis. Overall Nano3P seq is a simple and robust method for accurately estimating transcript levels tail lengths and tail composition heterogeneity in individual reads with minimal library preparation biases both in the coding and non coding transcriptome. ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10   Zebrafish Ribodepleted RNA 2hpf 4hpf 6hpf Zebrafish Ribodepleted Rep1 SAMEA110100411 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10|External Id:SAMEA110100411|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 10 10T00:20:53Z|INSDC last update:2022 10 10T00:20:53Z|INSDC status:public|Submitter Id:Zebrafish Ribodepleted Rep1|common name:zebrafish|sample name:Zebrafish Ribodepleted Rep1                 MinION sequencing ena EXPERIMENT TAB 13 06 2022 16:07:52:807 813 cDNA786327 ZFRDR1 1     RNA-Seq TRANSCRIPTOMIC other SINGLE OXFORD_NANOPORE MinION   ERP138294 MinION sequencing ENA FIRST PUBLIC:2022 10 10|ENA LAST UPDATE:2022 10 10 cDNA786327_ZFRDR1.tar.gz nanopore 1900613556.0 1660167.0 ena RUN TAB 13 06 2022 16:07:52:807 814 0:1144.83 A:473050820;C:438054520;G:425169743;T:564338473;N:0 1144       473050820 438054520 425169743 564338473 0 ERX9385636 ERS12199236 ERA15547404 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont 3prime poly_a unknown bulk unknown unknown   Spain 2022-10-10 Multi-stage Embryo Undetermined Embryo Imprecise
11045 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
24546 24546 ERR964671 ERX1041634 ERS792101 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 SAMEA3484816 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|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 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 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-20091014-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-1cell_F3_QV.qual.gz SOLiD_native SOLiD_native 2625510200.0 52510204.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 5 0:50 0:677149824;1:606769571;2:761187530;3:578170290;.:2232985 50                 ERX1041634 ERS792101 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.71662   0.0994   0.91644   0.74578   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Zygote Embryo Undetermined Embryo Imprecise
24547 24547 ERR964670 ERX1041633 ERS792104 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 SAMEA3484819 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|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 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 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-20090709-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-50epiboly_F3_QV.qual.gz SOLiD_native SOLiD_native 5325942150.0 106518843.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 4 0:50 0:1376469323;1:1227617853;2:1499234750;3:1210700143;.:11920081 50                 ERX1041633 ERS792104 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.7059   0.10511   0.91492   0.75125   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Gastrula 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
24549 24549 ERR964667 ERX1041630 ERS792101 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 SAMEA3484816 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484816|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 1cell|common name:zebrafish|dev stage:1cell|sample name:KI BN JKE DRERIO RNASEQ 2009 1cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 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-20090709-1cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-1cell_F3_QV.qual.gz SOLiD_native SOLiD_native 5717685400.0 114353708.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 1 0:50 0:1643444976;1:1261570333;2:1504304496;3:1282815913;.:25549682 50                 ERX1041630 ERS792101 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.72274   0.11151   0.92348   0.71904   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Zygote Embryo Undetermined Embryo Imprecise
24550 24550 ERR964668 ERX1041631 ERS792102 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 SAMEA3484817 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|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 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:870 2 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-20090709-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20090709-16cell_F3_QV.qual.gz SOLiD_native SOLiD_native 5278508300.0 105570166.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:871 2 0:50 0:1410981717;1:1203936808;2:1415708111;3:1223403795;.:24477869 50                 ERX1041631 ERS792102 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.71371   0.09346   0.91539   0.73015   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Cleavage Embryo Undetermined Embryo Imprecise
24551 24551 ERR964674 ERX1041637 ERS792104 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 SAMEA3484819 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484819|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 50epiboly|common name:zebrafish|dev stage:50% epiboly|sample name:KI BN JKE DRERIO RNASEQ 2009 50epiboly|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 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-20091014-50epiboly_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-50epiboly_F3_QV.qual.gz SOLiD_native SOLiD_native 2541596650.0 50831933.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:873 8 0:50 0:670988333;1:585266057;2:708634642;3:574052618;.:2655000 50                 ERX1041637 ERS792104 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.72135   0.10529   0.90997   0.76049   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Gastrula 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
24553 24553 ERR964672 ERX1041635 ERS792102 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 SAMEA3484817 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION ENA first public:2015 07 16|ENA last update:2015 07 15|External Id:SAMEA3484817|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 16cell|common name:zebrafish|dev stage:16 cell|sample name:KI BN JKE DRERIO RNASEQ 2009 16cell|strain:Tuebingen                 AB SOLiD System 3.0 sequencing ena EXPERIMENT KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 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-20091014-16cell_F3.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-20091014-16cell_F3_QV.qual.gz SOLiD_native SOLiD_native 2719433200.0 54388664.0 ena RUN KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 15 07 2015 15:13:47:872 6 0:50 0:699731678;1:628745158;2:754903505;3:633574679;.:2478180 50                 ERX1041635 ERS792102 ERA458495 KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION|European Nucleotide Archive KAROLINSKA INSTITUTET DEPARTMENT OF BIOSCIENCES AND NUTRITION 1 0.73214   0.09566   0.90836   0.74043   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Sweden 2015-07-15 Cleavage Embryo Undetermined Embryo Imprecise
29719 29719 SRR27485664 SRX23156885 SRS20107306 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R3   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:3|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06009 EV06009 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06009.R1.fastq.gz fastq 809138488.0 10734286.0 EV06009.R1.fastq.gz 0:75.38 A:236901398;C:156814193;G:179647937;T:235732894;N:42066 75       236901398 156814193 179647937 235732894 42066 SRX23156885 SRS20107306 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.92159   0.07516   0.837   0.7566   69   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29730 29730 SRR27485675 SRX23156874 SRS20107295 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:2|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06002 EV06002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06002.R1.fastq.gz fastq 632849068.0 8404028.0 EV06002.R1.fastq.gz 0:75.30 A:194183801;C:123105421;G:139266843;T:176255048;N:37955 75       194183801 123105421 139266843 176255048 37955 SRX23156874 SRS20107295 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.88896   0.09385   0.81864   0.73385   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29737 29737 SRR27477297 SRX23148650 SRS20099368 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:4|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV09002 EV09002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV09002.R1.fastq.gz fastq 546999929.0 7270092.0 EV09002.R1.fastq.gz 0:75.24 A:165415993;C:110874896;G:124384517;T:146294099;N:30424 75       165415993 110874896 124384517 146294099 30424 SRX23148650 SRS20099368 SRA1782413 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.9065   0.11883   0.82231   0.74466   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-10 Undetermined 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
36668 36668 SRR800037 SRX257149 SRS405106 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 egg RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|dev stage:egg                 egg RNAseq totalRNARibominus egg RNAseq totalRNARibominus 7784X1 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         3584440000.0 71688800.0 7784X1 110323 SN141 0332 A81FDVABXX 8 0:50 A:1013532157;C:812179975;G:992916103;T:765761452;N:50313 50       1013532157 812179975 992916103 765761452 50313 SRX257149 SRS405106 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.87304   0.12853   0.81988   0.80407   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-01 Undetermined Embryo Undetermined Embryo Imprecise
36669 36669 SRR800038 SRX257149 SRS405106 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 egg RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|dev stage:egg                 egg RNAseq totalRNARibominus egg RNAseq totalRNARibominus 7784X1 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         2794240450.0 55884809.0 7784X1 110119 SN141 0323 B8162JABXX 8 0:50 A:792200981;C:632130044;G:772351331;T:596980885;N:577209 50       792200981 632130044 772351331 596980885 577209 SRX257149 SRS405106 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.86104   0.12909   0.82266   0.80894   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-01 Undetermined Embryo Undetermined Embryo Imprecise
58479 58479 SRR12436783 SRX8932472 SRS7188817 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   GEO accession GSM4724702 is currently private and is scheduled to be released on Mar 17 2023. GSM4724702     Ski7 FER R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB GSM4724702 GSM4724702: Ski7 FER R3 polyA; Danio rerio; RNA Seq GSM4724702   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724702 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_FER_R3_polyA.fastq fastq 1777842000.0 17778420.0 GSM4724702 r1 0:100 A:440367983;C:434184573;G:419300944;T:483847825;N:140675 100       440367983 434184573 419300944 483847825 140675 SRX8932472 SRS7188817 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96519   0.0558   0.79762   0.49071   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58480 58480 SRR12436782 SRX8932471 SRS7188816 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   GEO accession GSM4724701 is currently private and is scheduled to be released on Mar 17 2023. GSM4724701     Ski7 FER R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB GSM4724701 GSM4724701: Ski7 FER R2 polyA; Danio rerio; RNA Seq GSM4724701   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724701 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_FER_R2_polyA.fastq fastq 1580941100.0 15809411.0 GSM4724701 r1 0:100 A:393346905;C:386319994;G:375568338;T:425580399;N:125464 100       393346905 386319994 375568338 425580399 125464 SRX8932471 SRS7188816 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96387   0.06115   0.80251   0.48311   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58481 58481 SRR12436781 SRX8932470 SRS7188815 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 FER R1 polyA GSM4724700   tissue:zebrafish egg|genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB Ski7 FER R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:fertilized egg|strain:TLAB GSM4724700 GSM4724700: Ski7 FER R1 polyA; Danio rerio; RNA Seq GSM4724700   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724700 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_FER_R1_polyA.fastq fastq 2213300600.0 22133006.0 GSM4724700 r1 0:100 A:554108128;C:532528202;G:525489897;T:601097373;N:77000 100       554108128 532528202 525489897 601097373 77000 SRX8932470 SRS7188815 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96118   0.06109   0.8046   0.48546   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58482 58482 SRR12436780 SRX8932469 SRS7188814 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 ACT R3 polyA GSM4724699   tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB Ski7 ACT R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:activated egg|strain:TLAB GSM4724699 GSM4724699: Ski7 ACT R3 polyA; Danio rerio; RNA Seq GSM4724699   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724699 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_ACT_R3_polyA.fastq fastq 1922804200.0 19228042.0 GSM4724699 r1 0:100 A:480850703;C:463917366;G:452391538;T:525491911;N:152682 100       480850703 463917366 452391538 525491911 152682 SRX8932469 SRS7188814 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96391   0.0566   0.80046   0.48338   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58483 58483 SRR12436779 SRX8932468 SRS7188813 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 ACT R2 polyA GSM4724698   tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB Ski7 ACT R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:activated egg|strain:TLAB GSM4724698 GSM4724698: Ski7 ACT R2 polyA; Danio rerio; RNA Seq GSM4724698   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724698 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_ACT_R2_polyA.fastq fastq 1928647900.0 19286479.0 GSM4724698 r1 0:100 A:482751186;C:469163733;G:460738816;T:515841418;N:152747 100       482751186 469163733 460738816 515841418 152747 SRX8932468 SRS7188813 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96439   0.05875   0.80921   0.47651   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58484 58484 SRR12436778 SRX8932467 SRS7188812 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 ACT R1 polyA GSM4724697   tissue:zebrafish egg|genotype:ski7 / |developmental stage:activated egg|strain:TLAB Ski7 ACT R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:activated egg|strain:TLAB GSM4724697 GSM4724697: Ski7 ACT R1 polyA; Danio rerio; RNA Seq GSM4724697   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724697 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_ACT_R1_polyA.fastq fastq 1459115400.0 14591154.0 GSM4724697 r1 0:100 A:361126428;C:358381337;G:346060607;T:393431535;N:115493 100       361126428 358381337 346060607 393431535 115493 SRX8932467 SRS7188812 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96515   0.06732   0.80395   0.48544   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58485 58485 SRR12436777 SRX8932466 SRS7188811 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 INA R3 polyA GSM4724696   tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB Ski7 INA R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:inactive egg|strain:TLAB GSM4724696 GSM4724696: Ski7 INA R3 polyA; Danio rerio; RNA Seq GSM4724696   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724696 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_SQU_R3_polyA.fastq fastq 1063954100.0 10639541.0 GSM4724696 r1 0:100 A:265551085;C:258698639;G:249117151;T:290502423;N:84802 100       265551085 258698639 249117151 290502423 84802 SRX8932466 SRS7188811 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96171   0.05846   0.77346   0.49713   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58486 58486 SRR12436776 SRX8932465 SRS7188810 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 INA R2 polyA GSM4724695   tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB Ski7 INA R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:inactive egg|strain:TLAB GSM4724695 GSM4724695: Ski7 INA R2 polyA; Danio rerio; RNA Seq GSM4724695   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724695 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_SQU_R2_polyA.fastq fastq 12041609400.0 120416094.0 GSM4724695 r1 0:100 A:3032420667;C:2912793806;G:2864619397;T:3231646175;N:129355 100       3032420667 2912793806 2864619397 3231646175 129355 SRX8932465 SRS7188810 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.9612   0.0577   0.81091   0.48028   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58487 58487 SRR12436775 SRX8932464 SRS7188809 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   Ski7 INA R1 polyA GSM4724694   tissue:zebrafish egg|genotype:ski7 / |developmental stage:inactive egg|strain:TLAB Ski7 INA R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:ski7 / |developmental stage:inactive egg|strain:TLAB GSM4724694 GSM4724694: Ski7 INA R1 polyA; Danio rerio; RNA Seq GSM4724694   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724694 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     Ski7_Ooc_SQU_R1_polyA.fastq fastq 1017000600.0 10170006.0 GSM4724694 r1 0:100 A:250669909;C:250298820;G:241072052;T:274878959;N:80860 100       250669909 250298820 241072052 274878959 80860 SRX8932464 SRS7188809 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96496   0.05463   0.80592   0.47885   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58512 58512 SRR12436750 SRX8932439 SRS7188784 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT FER R3 polyA GSM4724669   tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB WT FER R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:fertilized egg|strain:TLAB GSM4724669 GSM4724669: WT FER R3 polyA; Danio rerio; RNA Seq GSM4724669   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724669 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_FER_R3_polyA.fastq fastq 6771381900.0 67713819.0 GSM4724669 r1 0:100 A:1749508781;C:1638169429;G:1570468624;T:1813188646;N:46420 100       1749508781 1638169429 1570468624 1813188646 46420 SRX8932439 SRS7188784 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96178   0.0557   0.8254   0.49638   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58513 58513 SRR12436749 SRX8932438 SRS7188783 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT FER R2 polyA GSM4724668   tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB WT FER R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:fertilized egg|strain:TLAB GSM4724668 GSM4724668: WT FER R2 polyA; Danio rerio; RNA Seq GSM4724668   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724668 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_FER_R2_polyA.fastq fastq 1061307000.0 10613070.0 GSM4724668 r1 0:100 A:257645591;C:262618152;G:256246632;T:284713098;N:83527 100       257645591 262618152 256246632 284713098 83527 SRX8932438 SRS7188783 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.97035   0.03791   0.81769   0.49181   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58514 58514 SRR12436748 SRX8932437 SRS7188782 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT FER R1 polyA GSM4724667   tissue:zebrafish egg|genotype:wild type|developmental stage:fertilized egg|strain:TLAB WT FER R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:fertilized egg|strain:TLAB GSM4724667 GSM4724667: WT FER R1 polyA; Danio rerio; RNA Seq GSM4724667   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724667 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_FER_R1_polyA.fastq fastq 1139600300.0 11396003.0 GSM4724667 r1 0:100 A:278063418;C:281065192;G:275555423;T:304826973;N:89294 100       278063418 281065192 275555423 304826973 89294 SRX8932437 SRS7188782 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96734   0.06497   0.81515   0.49598   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58515 58515 SRR12436747 SRX8932436 SRS7188781 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT ACT R3 polyA GSM4724666   tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB WT ACT R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:activated egg|strain:TLAB GSM4724666 GSM4724666: WT ACT R3 polyA; Danio rerio; RNA Seq GSM4724666   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724666 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_ACT_R3_polyA.fastq fastq 8285065900.0 82850659.0 GSM4724666 r1 0:100 A:2144352935;C:1997916723;G:1922332681;T:2220387512;N:76049 100       2144352935 1997916723 1922332681 2220387512 76049 SRX8932436 SRS7188781 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96318   0.06182   0.82511   0.49104   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58516 58516 SRR12436746 SRX8932435 SRS7188780 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT ACT R2 polyA GSM4724665   tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB WT ACT R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:activated egg|strain:TLAB GSM4724665 GSM4724665: WT ACT R2 polyA; Danio rerio; RNA Seq GSM4724665   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724665 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_ACT_R2_polyA.fastq fastq 1209882800.0 12098828.0 GSM4724665 r1 0:100 A:302800050;C:293974175;G:286616960;T:326395031;N:96584 100       302800050 293974175 286616960 326395031 96584 SRX8932435 SRS7188780 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96659   0.054   0.81694   0.49155   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58517 58517 SRR12436745 SRX8932434 SRS7188779 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT ACT R1 polyA GSM4724664   tissue:zebrafish egg|genotype:wild type|developmental stage:activated egg|strain:TLAB WT ACT R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:activated egg|strain:TLAB GSM4724664 GSM4724664: WT ACT R1 polyA; Danio rerio; RNA Seq GSM4724664   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724664 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_ACT_R1_polyA.fastq fastq 1664829900.0 16648299.0 GSM4724664 r1 0:100 A:407654756;C:407749206;G:401595821;T:447697470;N:132647 100       407654756 407749206 401595821 447697470 132647 SRX8932434 SRS7188779 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96622   0.06206   0.81477   0.49247   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58518 58518 SRR12436744 SRX8932433 SRS7188778 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT INA R3 polyA GSM4724663   tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB WT INA R3 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:inactive egg|strain:TLAB GSM4724663 GSM4724663: WT INA R3 polyA; Danio rerio; RNA Seq GSM4724663   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724663 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_SQU_R3_polyA.fastq fastq 7170278200.0 71702782.0 GSM4724663 r1 0:100 A:1852022154;C:1727198429;G:1664295627;T:1926714520;N:47470 100       1852022154 1727198429 1664295627 1926714520 47470 SRX8932433 SRS7188778 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96163   0.06005   0.81686   0.48888   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58519 58519 SRR12436743 SRX8932432 SRS7188777 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT INA R2 polyA GSM4724662   tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB WT INA R2 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:inactive egg|strain:TLAB GSM4724662 GSM4724662: WT INA R2 polyA; Danio rerio; RNA Seq GSM4724662   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724662 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_SQU_R2_polyA.fastq fastq 3912697500.0 39126975.0 GSM4724662 r1 0:100 A:975441132;C:951912258;G:931850781;T:1053181584;N:311745 100       975441132 951912258 931850781 1053181584 311745 SRX8932432 SRS7188777 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96632   0.05261   0.80685   0.49154   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
58520 58520 SRR12436742 SRX8932431 SRS7188776 SRP253077 PRJNA613025 Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition GSE147112 Transcriptome Analysis Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.   pubmed:33600438;pubmed:34556579   WT INA R1 polyA GSM4724661   tissue:zebrafish egg|genotype:wild type|developmental stage:inactive egg|strain:TLAB WT INA R1 polyA Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM zebrafish egg   Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle genotype:wild type|developmental stage:inactive egg|strain:TLAB GSM4724661 GSM4724661: WT INA R1 polyA; Danio rerio; RNA Seq GSM4724661   1 Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina GEO Accession:GSM4724661 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP253077     WT_Ooc_SQU_R1_polyA.fastq fastq 1688458000.0 16884580.0 GSM4724661 r1 0:100 A:417912368;C:413739954;G:398861614;T:457809401;N:134663 100       417912368 413739954 398861614 457809401 134663 SRX8932431 SRS7188776 SRA1055855 GEO Pauli lab, Research Institute of Molecular Pathology 1 0.96554   0.06045   0.81972   0.48378   100   B   usable mapping rate illumina hiseq_era unknown poly_a nebnext bulk unknown unknown   Austria 2020-08-12 Undetermined Embryo Undetermined Embryo Imprecise
60104 60104 SRR12142045 SRX8663215 SRS6944340 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 4   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 4 Dre 4 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g004_1.fastq.gz fastq 509713380.0 9994380.0 DreSceMix g004 1.fastq.gz 0:51 A:251366594;C:61585710;G:62159129;T:134578953;N:22994 51       251366594 61585710 62159129 134578953 22994 SRX8663215 SRS6944340 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.67392   0.54102   0.86476   0.37091   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60105 60105 SRR12141709 SRX8663075 SRS6944200 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 3   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 3 Dre 3 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g003_1.fastq.gz fastq 499717482.0 9798382.0 DreSceMix g003 1.fastq.gz 0:51 A:263221073;C:56114768;G:56547079;T:123812019;N:22543 51       263221073 56114768 56547079 123812019 22543 SRX8663075 SRS6944200 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.63258   0.48288   0.86819   0.35874   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60106 60106 SRR12141808 SRX8662976 SRS6944101 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 6   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 12 Dre 12 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g014_1.fastq.gz fastq 421063599.0 8256149.0 DreSceMix g014 1.fastq.gz 0:51 A:207118237;C:53600213;G:54041718;T:106284709;N:18722 51       207118237 53600213 54041718 106284709 18722 SRX8662976 SRS6944101 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.47999   0.19308   0.85977   0.46733   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60107 60107 SRR12141828 SRX8662956 SRS6944081 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 4   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 10 Dre 10 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g012_1.fastq.gz fastq 626464773.0 12283623.0 DreSceMix g012 1.fastq.gz 0:51 A:263307070;C:96744908;G:98635228;T:167749896;N:27671 51       263307070 96744908 98635228 167749896 27671 SRX8662956 SRS6944081 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.50608   0.14369   0.83422   0.45691   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60108 60108 SRR12141839 SRX8662945 SRS6944070 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 3   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 9 Dre 9 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g011_1.fastq.gz fastq 436381296.0 8556496.0 DreSceMix g011 1.fastq.gz 0:51 A:205579619;C:58008903;G:59021026;T:113752218;N:19530 51       205579619 58008903 59021026 113752218 19530 SRX8662945 SRS6944070 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.46615   0.18281   0.84778   0.44592   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60109 60109 SRR12141850 SRX8662934 SRS6944059 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 2   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 8 Dre 8 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g010_1.fastq.gz fastq 870727437.0 17073087.0 DreSceMix g010 1.fastq.gz 0:51 A:343772776;C:142428987;G:145570260;T:238917135;N:38279 51       343772776 142428987 145570260 238917135 38279 SRX8662934 SRS6944059 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.52883   0.1235   0.82256   0.45498   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60110 60110 SRR12141861 SRX8662923 SRS6944047 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 1   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 7 Dre 7 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g009_1.fastq.gz fastq 1875928206.0 36782906.0 DreSceMix g009 1.fastq.gz 0:51 A:684015713;C:329272255;G:335557540;T:526999083;N:83615 51       684015713 329272255 335557540 526999083 83615 SRX8662923 SRS6944047 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.58553   0.11315   0.8029   0.4678   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60111 60111 SRR12141872 SRX8662912 SRS6944037 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 6   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 6 Dre 6 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g006_1.fastq.gz fastq 390346044.0 7653844.0 DreSceMix g006 1.fastq.gz 0:51 A:194005234;C:46666192;G:46964771;T:102692143;N:17704 51       194005234 46666192 46964771 102692143 17704 SRX8662912 SRS6944037 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.69496   0.57077   0.86864   0.35451   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60112 60112 SRR12141959 SRX8662825 SRS6943950 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 5   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 5 Dre 5 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g005_1.fastq.gz fastq 684050964.0 13412764.0 DreSceMix g005 1.fastq.gz 0:51 A:318875237;C:88359396;G:89394558;T:187391266;N:30507 51       318875237 88359396 89394558 187391266 30507 SRX8662825 SRS6943950 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.61659   0.4142   0.8393   0.42049   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60113 60113 SRR12142001 SRX8662783 SRS6943908 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of purified RNA from lysate for Fig.S2   zebrafish purifiedRNA biological replicate 5   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:purified from lysate|fig:S2|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 11 Dre 11 cDNA was synthesized with the purified RNA. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g013_1.fastq.gz fastq 998754318.0 19583418.0 DreSceMix g013 1.fastq.gz 0:51 A:402091762;C:156702863;G:160047354;T:279867921;N:44418 51       402091762 156702863 160047354 279867921 44418 SRX8662783 SRS6943908 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.52766   0.13651   0.81237   0.45557   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60114 60114 SRR12142002 SRX8662782 SRS6943907 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 2   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 2 Dre 2 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g002_1.fastq.gz fastq 702610578.0 13776678.0 DreSceMix g002 1.fastq.gz 0:51 A:332485038;C:89482705;G:90437771;T:190173083;N:31981 51       332485038 89482705 90437771 190173083 31981 SRX8662782 SRS6943907 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.63597   0.45832   0.85088   0.40969   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
60115 60115 SRR12142003 SRX8662781 SRS6943906 SRP269853 PRJNA643885 performance test of DeLTa Seq PRJNA643885 Other This data set were used for development and performance evaluation of Direct lysate targeted RNA Seq DeLTa Seq     RNA Seq of lysate for FigS2   zebrafish lysate biological replicate 1   strain:AB|age:2 days|sex:hermaphrodite|tissue:whole|sample type:lysate|fig:S2|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 DeLTa Seq Dre 1 Dre 1 cDNA was synthesized with the lysate. Non targeted RNA Seq were conducted according to Lasy Seq ver. 1.1 protocol18 https://sites.google.com/view/lasy seq/.     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina HiSeq 2500   SRP269853     DreSceMix_g001_1.fastq.gz fastq 1273185777.0 24964427.0 DreSceMix g001 1.fastq.gz 0:51 A:541573299;C:186989405;G:191401487;T:353163815;N:57771 51       541573299 186989405 191401487 353163815 57771 SRX8662781 SRS6943906 SRA1094353 Ryukoku university|Fauculity of Agriculture Ryukoku university 1 0.62046   0.30937   0.8197   0.44014   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2020-07-03 Hatching Embryo Undetermined Embryo Imprecise
69604 69604 SRR18935955 SRX15013551 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81332 L81332 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-2_L7_I332.R1.clean.fastq.gz fastq 3448675800.0 22991172.0 Alad 2 L7 I332.R1.clean.fastq.gz 0:150 1:0 A:909204217;C:819708757;G:815883274;T:903292138;N:587414 150 0     909204217 819708757 815883274 903292138 587414 SRX15013551 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93973   0.13997   0.7685   0.51168   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69605 69605 SRR18935956 SRX15013550 SRS12762156 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alad RBC   strain:alad mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81331 L81331 FACS sorted alad mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alad-1_L8_I331.R1.clean.fastq.gz fastq 3987610500.0 26584070.0 Alad 1 L8 I331.R1.clean.fastq.gz 0:150 1:0 A:1031398922;C:974521107;G:967367126;T:1013951504;N:371841 150 0     1031398922 974521107 967367126 1013951504 371841 SRX15013550 SRS12762156 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.9447   0.1019   0.81286   0.58316   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69606 69606 SRR18935957 SRX15013549 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81330 L81330 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-2_L8_I330.R1.clean.fastq.gz fastq 4163915100.0 27759434.0 Alas2 2 L8 I330.R1.clean.fastq.gz 0:150 1:0 A:1119245849;C:968636914;G:967111308;T:1108544148;N:376881 150 0     1119245849 968636914 967111308 1108544148 376881 SRX15013549 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.92608   0.1778   0.75471   0.55161   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69607 69607 SRR18935958 SRX15013548 SRS12762155 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         alas2 RBC   strain:alas2 mutant|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81329 L81329 FACS sorted alas2 mutant RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     Alas2-1_L8_I329.R1.clean.fastq.gz fastq 3953391150.0 26355941.0 Alas2 1 L8 I329.R1.clean.fastq.gz 0:150 1:0 A:1035309566;C:950958591;G:946245209;T:1020520823;N:356961 150 0     1035309566 950958591 946245209 1020520823 356961 SRX15013548 SRS12762155 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.93024   0.14212   0.81213   0.61442   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69608 69608 SRR18935959 SRX15013547 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81328 L81328 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-2_L8_I328.R1.clean.fastq.gz fastq 3589015200.0 23926768.0 WT 2 L8 I328.R1.clean.fastq.gz 0:150 1:0 A:922300230;C:887849832;G:879590696;T:898942142;N:332300 150 0     922300230 887849832 879590696 898942142 332300 SRX15013547 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94576   0.09241   0.83514   0.68592   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula Embryo Undetermined Embryo Imprecise
69609 69609 SRR18935960 SRX15013546 SRS12762154 SRP372447 PRJNA832566 zebrafish RBC sequencing PRJNA832566 Other profiling the distinct transcriptional identity of RBC from different RBC related mutants.         WT RBC   strain:WT|dev stage:36 hpf|sex:not collected|tissue:RBC|BioSampleModel:Model organism or animal                 RNA seq of RBC L81327 L81327 FACS sorted WT RBCs     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA Illumina NovaSeq 6000   SRP372447     WT-1_L8_I327.R1.clean.fastq.gz fastq 4062851700.0 27085678.0 WT 1 L8 I327.R1.clean.fastq.gz 0:150 1:0 A:1028410873;C:1020911876;G:1010215515;T:1002940085;N:373351 150 0     1028410873 1020911876 1010215515 1002940085 373351 SRX15013546 SRS12762154 SRA1410774 Chinese Acamedy of Sciences|Institute of zoology Chinese Acamedy of Sciences 1 0.94919   0.0692   0.85567   0.70156   150   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-04-27 Pharyngula 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");;