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364 rows where devstage_curation = "Cleavage" and tissue_curation = "Whole Organism"

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experiment.library_selection 6

technology 4

experiment.library_strategy 3

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 364 ✖

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Cleavage · 364 ✖
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
71 71 DRR032753 DRX029559 DRS049958 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 114 individuals Dr 8cell 2 SAMD00028150   sample name:Dr 8cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028150 DRX029559 Dr 8cell 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028150       3708921900.0 37089219.0 DRR032753 0:100 1:0 A:985502141;C:874161613;G:869551685;T:979663686;N:42775 100 0     985502141 874161613 869551685 979663686 42775 DRX029559 DRS049958 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.93329   0.02366   0.78896   0.47447   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
72 72 DRR032752 DRX029558 DRS049957 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 96 individuals Dr 8cell 1 SAMD00028149   sample name:Dr 8cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:8cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028149 DRX029558 Dr 8cell 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028149       3666991200.0 36669912.0 DRR032752 0:100 1:0 A:976118513;C:862559696;G:858017821;T:970254302;N:40868 100 0     976118513 862559696 858017821 970254302 40868 DRX029558 DRS049957 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.934   0.02403   0.78877   0.46902   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
86 86 DRR032738 DRX029544 DRS049943 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 100 individuals Dr 32cell 2 SAMD00028135   sample name:Dr 32cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028135 DRX029544 Dr 32cell 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028135       3678713000.0 36787130.0 DRR032738 0:100 1:0 A:981005900;C:863203049;G:859660640;T:974807835;N:35576 100 0     981005900 863203049 859660640 974807835 35576 DRX029544 DRS049943 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.93302   0.02468   0.77441   0.47485   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
87 87 DRR032737 DRX029543 DRS049942 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 95 individuals Dr 32cell 1 SAMD00028134   sample name:Dr 32cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:32cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028134 DRX029543 Dr 32cell 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028134       3870906500.0 38709065.0 DRR032737 0:100 1:0 A:1030407751;C:909948718;G:905608620;T:1024897443;N:43968 100 0     1030407751 909948718 905608620 1024897443 43968 DRX029543 DRS049942 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.93364   0.02484   0.77307   0.47588   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
90 90 DRR032734 DRX029540 DRS049939 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 107 individuals Dr 2cell 2 SAMD00028131   sample name:Dr 2cell 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028131 DRX029540 Dr 2cell 2 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028131       3687517000.0 36875170.0 DRR032734 0:100 1:0 A:975272080;C:873518282;G:869743434;T:968941851;N:41353 100 0     975272080 873518282 869743434 968941851 41353 DRX029540 DRS049939 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.93204   0.02088   0.81639   0.47553   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
91 91 DRR032733 DRX029539 DRS049938 DRP003810 PRJDB3785 EXPANDE project DRP003810 Other EXPression AloNg Development and Evolution EXPANDE project aims to identify gene expression profiles expanded during embryogenesis and evolution. In brief taking advantages of Illumina sequencing RNAseq profiles of early to late embryos of 8 chordate species were identified with biological replicates two or more biological replicates.     mRNA extracted from pooled embryos of 108 individuals Dr 2cell 1 SAMD00028130   sample name:Dr 2cell 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:2cell|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028130 DRX029539 Dr 2cell 1 1 Total RNA QIAGEN RNeasy followed by TruSeq   RNA-Seq TRANSCRIPTOMIC other SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003810 Illumina HiSeq 2000 sequencing of SAMD00028130       4156651100.0 41566511.0 DRR032733 0:100 1:0 A:1099943617;C:985498415;G:978884426;T:1092278665;N:45977 100 0     1099943617 985498415 978884426 1092278665 45977 DRX029539 DRS049938 DRA003460 UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo UT-BS|Lab for embryology, Department of Biological Sciences, University of Tokyo 1 0.93452   0.02198   0.81197   0.47342   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Cleavage Embryo Whole Organism All anatomical structures
3155 3155 ERR1410225 ERX1481464 ERS1021813 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool12 SAMEA3714664 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714664|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:11Z|INSDC status:public|Submitter Id:e9237f50 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTCAGCTC is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e9237f50 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#24 15565967 Illumina sequencing of library 15565967 constructed from sample accession ERS1021813 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TTCAGCTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#24.cram cram 682856330.0 5252741.0 SC RUN 18730 4#24 0:55 1:75 A:168217714;C:139075008;G:141169282;T:234338870;N:55456 55 75     168217714 139075008 141169282 234338870 55456 ERX1481464 ERS1021813 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.22601 0.6266 0.06302 0.07433 0.95848 0.87767 0.77147 0.72121 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3156 3156 ERR1410224 ERX1481463 ERS1021812 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool11 SAMEA3714663 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714663|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:10Z|INSDC status:public|Submitter Id:e91834b0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TACTAGTC is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e91834b0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#23 15565966 Illumina sequencing of library 15565966 constructed from sample accession ERS1021812 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TACTAGTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#23.cram cram 784669730.0 6035921.0 SC RUN 18730 4#23 0:55 1:75 A:193369040;C:154930839;G:157589012;T:278718023;N:62816 55 75     193369040 154930839 157589012 278718023 62816 ERX1481463 ERS1021812 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.22113 0.66423 0.05856 0.07177 0.95899 0.86705 0.76036 0.71777 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3157 3157 ERR1410223 ERX1481462 ERS1021811 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool10 SAMEA3714662 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714662|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:10Z|INSDC status:public|Submitter Id:e90c9bf0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCAGATTC is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e90c9bf0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#22 15565965 Illumina sequencing of library 15565965 constructed from sample accession ERS1021811 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCAGATTC. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#22.cram cram 1247901590.0 9599243.0 SC RUN 18730 4#22 0:55 1:75 A:314703461;C:244320464;G:241561095;T:447214667;N:101903 55 75     314703461 244320464 241561095 447214667 101903 ERX1481462 ERS1021811 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.20694 0.62963 0.04856 0.05487 0.95763 0.87026 0.7137 0.71273 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3158 3158 ERR1410222 ERX1481461 ERS1021810 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool9 SAMEA3714661 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714661|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:09Z|INSDC status:public|Submitter Id:e8fe4410 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TATGCCAG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8fe4410 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#21 15565964 Illumina sequencing of library 15565964 constructed from sample accession ERS1021810 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TATGCCAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#21.cram cram 1160974880.0 8930576.0 SC RUN 18730 4#21 0:55 1:75 A:287583127;C:233701395;G:225242195;T:414354028;N:94135 55 75     287583127 233701395 225242195 414354028 94135 ERX1481461 ERS1021810 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.20242 0.60852 0.05828 0.06484 0.95568 0.87456 0.67452 0.38749 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3159 3159 ERR1410221 ERX1481460 ERS1021809 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool8 SAMEA3714660 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714660|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:08Z|INSDC status:public|Submitter Id:e8f2d260 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGGCTCAG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8f2d260 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#20 15565963 Illumina sequencing of library 15565963 constructed from sample accession ERS1021809 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TGGCTCAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#20.cram cram 1041644630.0 8012651.0 SC RUN 18730 4#20 0:55 1:75 A:250361997;C:216927117;G:209137594;T:365137042;N:80880 55 75     250361997 216927117 209137594 365137042 80880 ERX1481460 ERS1021809 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.23722 0.6381 0.05317 0.07562 0.95503 0.87671 0.75995 0.72353 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3160 3160 ERR1410220 ERX1481459 ERS1021808 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool7 SAMEA3714659 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714659|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:08Z|INSDC status:public|Submitter Id:e8e787c0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCATTGAG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8e787c0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#19 15565962 Illumina sequencing of library 15565962 constructed from sample accession ERS1021808 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCATTGAG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#19.cram cram 1002402180.0 7710786.0 SC RUN 18730 4#19 0:55 1:75 A:249654737;C:203437995;G:194586976;T:354640685;N:81787 55 75     249654737 203437995 194586976 354640685 81787 ERX1481459 ERS1021808 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.21081 0.61197 0.04352 0.05852 0.9529 0.86815 0.65385 0.64824 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3161 3161 ERR1410219 ERX1481458 ERS1021807 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool6 SAMEA3714658 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714658|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:07Z|INSDC status:public|Submitter Id:e8dc3d20 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGTATGCG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8dc3d20 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#18 15565961 Illumina sequencing of library 15565961 constructed from sample accession ERS1021807 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TGTATGCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#18.cram cram 1001271050.0 7702085.0 SC RUN 18730 4#18 0:55 1:75 A:249131077;C:206043698;G:193568917;T:352446609;N:80749 55 75     249131077 206043698 193568917 352446609 80749 ERX1481458 ERS1021807 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.22004 0.6117 0.05313 0.0656 0.95095 0.8758 0.70135 0.69364 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3162 3162 ERR1410218 ERX1481457 ERS1021806 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool5 SAMEA3714657 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714657|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:06Z|INSDC status:public|Submitter Id:e8b183a0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCCAGTCG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8b183a0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#17 15565960 Illumina sequencing of library 15565960 constructed from sample accession ERS1021806 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCCAGTCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#17.cram cram 1240938140.0 9545678.0 SC RUN 18730 4#17 0:55 1:75 A:302318036;C:249218633;G:246601321;T:442702025;N:98125 55 75     302318036 249218633 246601321 442702025 98125 ERX1481457 ERS1021806 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.23057 0.63523 0.05319 0.067 0.95213 0.86695 0.69753 0.68537 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3163 3163 ERR1410217 ERX1481456 ERS1021805 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool4 SAMEA3714656 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714656|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:06Z|INSDC status:public|Submitter Id:e8ab9030 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAAGTTCG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8ab9030 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#16 15565959 Illumina sequencing of library 15565959 constructed from sample accession ERS1021805 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TAAGTTCG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#16.cram cram 942829030.0 7252531.0 SC RUN 18730 4#16 0:55 1:75 A:225274547;C:196341691;G:188483755;T:332654028;N:75009 55 75     225274547 196341691 188483755 332654028 75009 ERX1481456 ERS1021805 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.21889 0.64365 0.04363 0.07265 0.95181 0.87478 0.70501 0.69162 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3164 3164 ERR1410216 ERX1481455 ERS1021804 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool3 SAMEA3714655 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714655|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:05Z|INSDC status:public|Submitter Id:e8a5eae0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCAGGAGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8a5eae0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#15 15565958 Illumina sequencing of library 15565958 constructed from sample accession ERS1021804 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCAGGAGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#15.cram cram 992671030.0 7635931.0 SC RUN 18730 4#15 0:55 1:75 A:241776762;C:210080049;G:195284057;T:345448849;N:81313 55 75     241776762 210080049 195284057 345448849 81313 ERX1481455 ERS1021804 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.21439 0.6195 0.04725 0.05379 0.95191 0.87606 0.67336 0.65016 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3165 3165 ERR1410215 ERX1481454 ERS1021803 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool2 SAMEA3714654 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714654|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:05Z|INSDC status:public|Submitter Id:e89cc320 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCTCACGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e89cc320 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#14 15565957 Illumina sequencing of library 15565957 constructed from sample accession ERS1021803 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCTCACGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#14.cram cram 1234311910.0 9494707.0 SC RUN 18730 4#14 0:55 1:75 A:301439259;C:257228602;G:244500849;T:431043241;N:99959 55 75     301439259 257228602 244500849 431043241 99959 ERX1481454 ERS1021803 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.19348 0.62337 0.04021 0.05986 0.95574 0.87941 0.67064 0.69696 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3166 3166 ERR1410214 ERX1481453 ERS1021802 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 pool1 SAMEA3714653 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714653|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:04Z|INSDC status:public|Submitter Id:e897ba10 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a pool of 8 wild type zebrafish embryos from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TACTTCGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e897ba10 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#13 15565956 Illumina sequencing of library 15565956 constructed from sample accession ERS1021802 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TACTTCGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#13.cram cram 1039867140.0 7998978.0 SC RUN 18730 4#13 0:55 1:75 A:252384576;C:218519074;G:206578085;T:362298880;N:86525 55 75     252384576 218519074 206578085 362298880 86525 ERX1481453 ERS1021802 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.18713 0.60956 0.05049 0.0817 0.95556 0.87618 0.66594 0.68034 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3167 3167 ERR1410213 ERX1481452 ERS1021801 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 12 SAMEA3714652 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714652|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:04Z|INSDC status:public|Submitter Id:e89262e0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGAACTGG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e89262e0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#12 15565955 Illumina sequencing of library 15565955 constructed from sample accession ERS1021801 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TGAACTGG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#12.cram cram 1071792020.0 8244554.0 SC RUN 18730 4#12 0:55 1:75 A:266291261;C:216074486;G:207838804;T:381495628;N:91841 55 75     266291261 216074486 207838804 381495628 91841 ERX1481452 ERS1021801 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.19027 0.64477 0.0489 0.06997 0.95268 0.86371 0.66594 0.67162 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3168 3168 ERR1410212 ERX1481451 ERS1021800 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 11 SAMEA3714651 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714651|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:03Z|INSDC status:public|Submitter Id:e88d59d0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTGGTATG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e88d59d0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#11 15565954 Illumina sequencing of library 15565954 constructed from sample accession ERS1021800 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TTGGTATG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#11.cram cram 686164570.0 5278189.0 SC RUN 18730 4#11 0:55 1:75 A:165352345;C:146328635;G:134343947;T:240083817;N:55826 55 75     165352345 146328635 134343947 240083817 55826 ERX1481451 ERS1021800 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.22823 0.61844 0.08567 0.10696 0.95106 0.86797 0.62805 0.63179 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3169 3169 ERR1410211 ERX1481450 ERS1021799 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 10 SAMEA3714650 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714650|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:03Z|INSDC status:public|Submitter Id:e88829b0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAACGCTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e88829b0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#10 15565953 Illumina sequencing of library 15565953 constructed from sample accession ERS1021799 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TAACGCTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#10.cram cram 889043870.0 6838799.0 SC RUN 18730 4#10 0:55 1:75 A:223435089;C:179282347;G:171273337;T:314981588;N:71509 55 75     223435089 179282347 171273337 314981588 71509 ERX1481450 ERS1021799 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.19054 0.6472 0.0467 0.06495 0.953 0.86519 0.68221 0.68725 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3170 3170 ERR1410210 ERX1481449 ERS1021798 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 9 SAMEA3714649 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714649|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:02Z|INSDC status:public|Submitter Id:e88320a0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCGAAGTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e88320a0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#9 15565952 Illumina sequencing of library 15565952 constructed from sample accession ERS1021798 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCGAAGTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#9.cram cram 987809940.0 7598538.0 SC RUN 18730 4#9 0:55 1:75 A:248484130;C:197140774;G:188385871;T:353715305;N:83860 55 75     248484130 197140774 188385871 353715305 83860 ERX1481449 ERS1021798 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.2215 0.62639 0.05009 0.06362 0.94959 0.86689 0.63702 0.63984 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3171 3171 ERR1410209 ERX1481448 ERS1021797 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 8 SAMEA3714648 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714648|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:02Z|INSDC status:public|Submitter Id:e87d5440 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTCCATTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e87d5440 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#8 15565951 Illumina sequencing of library 15565951 constructed from sample accession ERS1021797 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TTCCATTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#8.cram cram 991993340.0 7630718.0 SC RUN 18730 4#8 0:55 1:75 A:248601530;C:201637312;G:190701521;T:350971271;N:81706 55 75     248601530 201637312 190701521 350971271 81706 ERX1481448 ERS1021797 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.18071 0.60546 0.04372 0.05614 0.95556 0.87182 0.64904 0.68316 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3172 3172 ERR1410208 ERX1481447 ERS1021796 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 7 SAMEA3714647 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714647|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:01Z|INSDC status:public|Submitter Id:e871e290 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAGTCTTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e871e290 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#7 15565950 Illumina sequencing of library 15565950 constructed from sample accession ERS1021796 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TAGTCTTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#7.cram cram 1355591770.0 10427629.0 SC RUN 18730 4#7 0:55 1:75 A:333761549;C:285155703;G:270975293;T:465589806;N:109419 55 75     333761549 285155703 270975293 465589806 109419 ERX1481447 ERS1021796 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.19403 0.63995 0.03449 0.07104 0.957 0.88641 0.73288 0.71598 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3173 3173 ERR1410207 ERX1481446 ERS1021795 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 6 SAMEA3714646 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714646|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:01Z|INSDC status:public|Submitter Id:e86670e0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGTGGTTG is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e86670e0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#6 15565949 Illumina sequencing of library 15565949 constructed from sample accession ERS1021795 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TGTGGTTG. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#6.cram cram 1121411330.0 8626241.0 SC RUN 18730 4#6 0:55 1:75 A:275436070;C:245845272;G:219970219;T:380067436;N:92333 55 75     275436070 245845272 219970219 380067436 92333 ERX1481446 ERS1021795 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.185 0.59026 0.03934 0.06143 0.95268 0.88968 0.59393 0.69736 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3174 3174 ERR1410206 ERX1481445 ERS1021794 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 5 SAMEA3714645 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714645|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:01Z|INSDC status:public|Submitter Id:e85b2640 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TCCTCAAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e85b2640 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#5 15565948 Illumina sequencing of library 15565948 constructed from sample accession ERS1021794 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TCCTCAAT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#5.cram cram 852544290.0 6558033.0 SC RUN 18730 4#5 0:55 1:75 A:202033234;C:177211087;G:169900063;T:303332405;N:67501 55 75     202033234 177211087 169900063 303332405 67501 ERX1481445 ERS1021794 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.21445 0.62891 0.0753 0.09655 0.95278 0.86929 0.61569 0.48656 55 75 T B mate1 technical by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3175 3175 ERR1410205 ERX1481444 ERS1021793 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 4 SAMEA3714644 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714644|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:42:00Z|INSDC status:public|Submitter Id:e84f8d80 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TACAGGAT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e84f8d80 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#4 15565947 Illumina sequencing of library 15565947 constructed from sample accession ERS1021793 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TACAGGAT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#4.cram cram 989803880.0 7613876.0 SC RUN 18730 4#4 0:55 1:75 A:241562947;C:196888151;G:193862254;T:357404172;N:86356 55 75     241562947 196888151 193862254 357404172 86356 ERX1481444 ERS1021793 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.27131 0.63988 0.04128 0.04919 0.95923 0.88292 0.81011 0.7508 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3176 3176 ERR1410204 ERX1481443 ERS1021792 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 3 SAMEA3714643 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714643|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:42:00Z|INSDC status:public|Submitter Id:e8441bd0 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TAGTGACT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8441bd0 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#3 15565946 Illumina sequencing of library 15565946 constructed from sample accession ERS1021792 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TAGTGACT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#3.cram cram 1144202930.0 8801561.0 SC RUN 18730 4#3 0:55 1:75 A:278906912;C:230946498;G:229591661;T:404660425;N:97434 55 75     278906912 230946498 229591661 404660425 97434 ERX1481443 ERS1021792 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.24055 0.6437 0.04616 0.05861 0.9554 0.88221 0.30306 0.73916 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3177 3177 ERR1410203 ERX1481442 ERS1021791 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 2 SAMEA3714642 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714642|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:44Z|INSDC last update:2015 12 16T13:41:59Z|INSDC status:public|Submitter Id:e8385c00 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TTCCTGCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e8385c00 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#2 15565945 Illumina sequencing of library 15565945 constructed from sample accession ERS1021791 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TTCCTGCT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#2.cram cram 1459339960.0 11225692.0 SC RUN 18730 4#2 0:55 1:75 A:361580033;C:294777861;G:295641568;T:507221717;N:118781 55 75     361580033 294777861 295641568 507221717 118781 ERX1481442 ERS1021791 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.25446 0.64481 0.04258 0.05864 0.95473 0.88562 0.32211 0.75437 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3178 3178 ERR1410202 ERX1481441 ERS1021790 ERP013756 PRJEB12296 Baseline expression from transcriptional profiling of zebrafish developmental stages 2 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_2-sc-4029 Transcriptome Analysis Paired end sequence data from the IlluminaHiSeq was prepared from RNA of wild type zebrafish embryos at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 453     ZMP phenotype 128 1 1 SAMEA3714641 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 10|ENA last update:2015 12 16|External Id:SAMEA3714641|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 10T14:31:45Z|INSDC last update:2015 12 16T13:41:58Z|INSDC status:public|Submitter Id:e73ff240 a000 11e5 800b 68b59976a382|common name:zebrafish|sample description:3 prime end enriched mRNA from a single wild type zebrafish embryo from ZMP phenotype 128 clutch 1 collected at cleavage 2 cell stage plus ERCC spike mix 2 Ambion. A 8 base indexing sequence TGCGATCT is bases 13 to 20 of read 1 followed by CG and polyT.|sample name:e73ff240 a000 11e5 800b 68b59976a382|strain:mixed                 Illumina HiSeq 2000 paired end sequencing SC EXP 18730 4#1 15565944 Illumina sequencing of library 15565944 constructed from sample accession ERS1021790 for study accession ERP013756. This is part of an Illumina multiplexed sequencing run 18730 4. This submission includes reads tagged with the sequence TGCGATCT. Transcriptome counting qPCR only   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP013756 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2016 05 10|ENA LAST UPDATE:2018 11 16 18730_4#1.cram cram 869624210.0 6689417.0 SC RUN 18730 4#1 0:55 1:75 A:211816407;C:178380016;G:176641186;T:302714073;N:72528 55 75     211816407 178380016 176641186 302714073 72528 ERX1481441 ERS1021790 ERA620320 European Nucleotide Archive Wellcome Sanger Institute 2 0.26789 0.63129 0.0568 0.09239 0.95978 0.88978 0.82999 0.78005 55 75 B B mate1-mate2 similar by mapping diff illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   United Kingdom 2015-12-16 Cleavage Embryo Whole Organism All anatomical structures
3788 3788 ERR1442900 ERX1513277 ERS1079219 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 F SAMEA3892085 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892085|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:07Z|INSDC status:public|Submitter Id:744149e0 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:744149e0 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 2#70 16564972 Illumina sequencing of library 16564972 constructed from sample accession ERS1079219 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 2. This submission includes reads tagged with the sequence GATCTCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_2#70.cram cram 364410400.0 1822052.0 SC RUN 19912 2#70 0:100 1:100 A:96471898;C:85460940;G:85739185;T:96152266;N:586111 100 100     96471898 85460940 85739185 96152266 586111 ERX1513277 ERS1079219 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96377 0.96719 0.0976 0.09955 0.79667 0.79693 0.58832 0.58226 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3789 3789 ERR1442899 ERX1513276 ERS1079218 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 E SAMEA3892084 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892084|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74358a10 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74358a10 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 2#69 16564960 Illumina sequencing of library 16564960 constructed from sample accession ERS1079218 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 2. This submission includes reads tagged with the sequence GGTGAGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_2#69.cram cram 312144800.0 1560724.0 SC RUN 19912 2#69 0:100 1:100 A:82044388;C:74027006;G:73985684;T:81583681;N:504041 100 100     82044388 74027006 73985684 81583681 504041 ERX1513276 ERS1079218 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96275 0.9677 0.10631 0.10791 0.79496 0.79535 0.57643 0.57303 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3790 3790 ERR1442898 ERX1513275 ERS1079217 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 D SAMEA3892083 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892083|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74295510 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74295510 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 2#68 16564948 Illumina sequencing of library 16564948 constructed from sample accession ERS1079217 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 2. This submission includes reads tagged with the sequence TGCGTGAA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_2#68.cram cram 330453000.0 1652265.0 SC RUN 19912 2#68 0:100 1:100 A:87696659;C:77248972;G:77394239;T:87578108;N:535022 100 100     87696659 77248972 77394239 87578108 535022 ERX1513275 ERS1079217 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96171 0.96419 0.10779 0.11047 0.79902 0.80018 0.57383 0.56925 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3791 3791 ERR1442897 ERX1513274 ERS1079216 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 C SAMEA3892082 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892082|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:741d9540 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 2#67 16564936 Illumina sequencing of library 16564936 constructed from sample accession ERS1079216 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 2. This submission includes reads tagged with the sequence TACCACCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_2#67.cram cram 327261000.0 1636305.0 SC RUN 19912 2#67 0:100 1:100 A:87523901;C:75771535;G:75871608;T:87573282;N:520674 100 100     87523901 75771535 75871608 87573282 520674 ERX1513274 ERS1079216 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.95986 0.96354 0.1123 0.11468 0.80156 0.80229 0.58372 0.58338 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3792 3792 ERR1442896 ERX1513273 ERS1079215 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 B SAMEA3892081 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 2#66 16564924 Illumina sequencing of library 16564924 constructed from sample accession ERS1079215 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 2. This submission includes reads tagged with the sequence TGAAGCCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_2#66.cram cram 328496600.0 1642483.0 SC RUN 19912 2#66 0:100 1:100 A:86841947;C:77278436;G:77262516;T:86589805;N:523896 100 100     86841947 77278436 77262516 86589805 523896 ERX1513273 ERS1079215 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96091 0.96535 0.1279 0.13047 0.79805 0.79857 0.58551 0.58209 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3878 3878 ERR1442810 ERX1513187 ERS1079219 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 F SAMEA3892085 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892085|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:07Z|INSDC status:public|Submitter Id:744149e0 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:744149e0 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 1#70 16564972 Illumina sequencing of library 16564972 constructed from sample accession ERS1079219 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 1. This submission includes reads tagged with the sequence GATCTCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_1#70.cram cram 364912600.0 1824563.0 SC RUN 19912 1#70 0:100 1:100 A:96642496;C:85588675;G:85883202;T:96301393;N:496834 100 100     96642496 85588675 85883202 96301393 496834 ERX1513187 ERS1079219 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96362 0.96689 0.09725 0.09882 0.79592 0.79703 0.59097 0.5784 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3879 3879 ERR1442809 ERX1513186 ERS1079218 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 E SAMEA3892084 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892084|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74358a10 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74358a10 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 1#69 16564960 Illumina sequencing of library 16564960 constructed from sample accession ERS1079218 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 1. This submission includes reads tagged with the sequence GGTGAGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_1#69.cram cram 312470400.0 1562352.0 SC RUN 19912 1#69 0:100 1:100 A:82160555;C:74100532;G:74069193;T:81696066;N:444054 100 100     82160555 74100532 74069193 81696066 444054 ERX1513186 ERS1079218 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96376 0.96859 0.10642 0.1079 0.79417 0.79474 0.5752 0.57 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3880 3880 ERR1442808 ERX1513185 ERS1079217 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 D SAMEA3892083 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892083|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74295510 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74295510 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 1#68 16564948 Illumina sequencing of library 16564948 constructed from sample accession ERS1079217 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 1. This submission includes reads tagged with the sequence TGCGTGAA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_1#68.cram cram 330554000.0 1652770.0 SC RUN 19912 1#68 0:100 1:100 A:87747224;C:77298685;G:77439701;T:87616982;N:451408 100 100     87747224 77298685 77439701 87616982 451408 ERX1513185 ERS1079217 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96163 0.96436 0.10875 0.1111 0.79928 0.79965 0.57561 0.5708 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3881 3881 ERR1442807 ERX1513184 ERS1079216 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 C SAMEA3892082 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892082|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:741d9540 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 1#67 16564936 Illumina sequencing of library 16564936 constructed from sample accession ERS1079216 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 1. This submission includes reads tagged with the sequence TACCACCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_1#67.cram cram 327019400.0 1635097.0 SC RUN 19912 1#67 0:100 1:100 A:87453957;C:75726607;G:75847551;T:87546870;N:444415 100 100     87453957 75726607 75847551 87546870 444415 ERX1513184 ERS1079216 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96147 0.9625 0.11258 0.11475 0.79825 0.79924 0.58372 0.56917 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3882 3882 ERR1442806 ERX1513183 ERS1079215 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 B SAMEA3892081 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19912 1#66 16564924 Illumina sequencing of library 16564924 constructed from sample accession ERS1079215 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19912 1. This submission includes reads tagged with the sequence TGAAGCCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19912_1#66.cram cram 327613800.0 1638069.0 SC RUN 19912 1#66 0:100 1:100 A:86594522;C:77121933;G:77114321;T:86338082;N:444942 100 100     86594522 77121933 77114321 86338082 444942 ERX1513183 ERS1079215 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.9614 0.96527 0.12823 0.13043 0.79762 0.79922 0.58597 0.5851 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3968 3968 ERR1442720 ERX1513097 ERS1079219 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 F SAMEA3892085 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892085|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:07Z|INSDC status:public|Submitter Id:744149e0 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:744149e0 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 2#70 16564972 Illumina sequencing of library 16564972 constructed from sample accession ERS1079219 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 2. This submission includes reads tagged with the sequence GATCTCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_2#70.cram cram 371283800.0 1856419.0 SC RUN 19850 2#70 0:100 1:100 A:98443439;C:87187703;G:87417381;T:98100142;N:135135 100 100     98443439 87187703 87417381 98100142 135135 ERX1513097 ERS1079219 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96411 0.96451 0.09692 0.09902 0.79657 0.7964 0.58932 0.57779 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3969 3969 ERR1442719 ERX1513096 ERS1079218 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 E SAMEA3892084 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892084|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74358a10 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74358a10 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 2#69 16564960 Illumina sequencing of library 16564960 constructed from sample accession ERS1079218 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 2. This submission includes reads tagged with the sequence GGTGAGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_2#69.cram cram 318491400.0 1592457.0 SC RUN 19850 2#69 0:100 1:100 A:83845999;C:75642375;G:75561647;T:83330437;N:110942 100 100     83845999 75642375 75561647 83330437 110942 ERX1513096 ERS1079218 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96388 0.96834 0.10544 0.10741 0.79336 0.79417 0.57217 0.56939 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3970 3970 ERR1442718 ERX1513095 ERS1079217 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 D SAMEA3892083 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892083|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74295510 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74295510 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 2#68 16564948 Illumina sequencing of library 16564948 constructed from sample accession ERS1079217 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 2. This submission includes reads tagged with the sequence TGCGTGAA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_2#68.cram cram 335548800.0 1677744.0 SC RUN 19850 2#68 0:100 1:100 A:89188408;C:78543202;G:78653253;T:89044211;N:119726 100 100     89188408 78543202 78653253 89044211 119726 ERX1513095 ERS1079217 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96211 0.96612 0.10777 0.11055 0.79724 0.79876 0.57249 0.43044 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3971 3971 ERR1442717 ERX1513094 ERS1079216 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 C SAMEA3892082 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892082|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:741d9540 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 2#67 16564936 Illumina sequencing of library 16564936 constructed from sample accession ERS1079216 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 2. This submission includes reads tagged with the sequence TACCACCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_2#67.cram cram 331952200.0 1659761.0 SC RUN 19850 2#67 0:100 1:100 A:88872903;C:76957606;G:77065688;T:88935012;N:120991 100 100     88872903 76957606 77065688 88935012 120991 ERX1513094 ERS1079216 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96191 0.96393 0.11342 0.11468 0.799 0.79908 0.58219 0.58045 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
3972 3972 ERR1442716 ERX1513093 ERS1079215 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 B SAMEA3892081 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 2#66 16564924 Illumina sequencing of library 16564924 constructed from sample accession ERS1079215 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 2. This submission includes reads tagged with the sequence TGAAGCCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_2#66.cram cram 333024200.0 1665121.0 SC RUN 19850 2#66 0:100 1:100 A:88172616;C:78454066;G:78393792;T:87885914;N:117812 100 100     88172616 78454066 78393792 87885914 117812 ERX1513093 ERS1079215 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96249 0.96556 0.1289 0.13166 0.79945 0.79961 0.58336 0.58063 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
4058 4058 ERR1442630 ERX1513007 ERS1079219 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 F SAMEA3892085 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892085|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:07Z|INSDC status:public|Submitter Id:744149e0 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:744149e0 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 1#70 16564972 Illumina sequencing of library 16564972 constructed from sample accession ERS1079219 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 1. This submission includes reads tagged with the sequence GATCTCTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_1#70.cram cram 371578800.0 1857894.0 SC RUN 19850 1#70 0:100 1:100 A:98533022;C:87264222;G:87555118;T:98151909;N:74529 100 100     98533022 87264222 87555118 98151909 74529 ERX1513007 ERS1079219 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.9636 0.96761 0.09699 0.09916 0.79525 0.79553 0.58618 0.57988 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
4059 4059 ERR1442629 ERX1513006 ERS1079218 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 E SAMEA3892084 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892084|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74358a10 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74358a10 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 1#69 16564960 Illumina sequencing of library 16564960 constructed from sample accession ERS1079218 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 1. This submission includes reads tagged with the sequence GGTGAGTT. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_1#69.cram cram 318342200.0 1591711.0 SC RUN 19850 1#69 0:100 1:100 A:83801083;C:75621628;G:75578752;T:83271737;N:69000 100 100     83801083 75621628 75578752 83271737 69000 ERX1513006 ERS1079218 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96351 0.96877 0.10486 0.10713 0.79423 0.79444 0.57288 0.57375 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
4060 4060 ERR1442628 ERX1513005 ERS1079217 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 D SAMEA3892083 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892083|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:74295510 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74295510 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 1#68 16564948 Illumina sequencing of library 16564948 constructed from sample accession ERS1079217 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 1. This submission includes reads tagged with the sequence TGCGTGAA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_1#68.cram cram 334846000.0 1674230.0 SC RUN 19850 1#68 0:100 1:100 A:88989528;C:78413149;G:78541907;T:88833028;N:68388 100 100     88989528 78413149 78541907 88833028 68388 ERX1513005 ERS1079217 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96197 0.96681 0.10873 0.11111 0.79805 0.7992 0.57474 0.57198 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
4061 4061 ERR1442627 ERX1513004 ERS1079216 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 C SAMEA3892082 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892082|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:06Z|INSDC status:public|Submitter Id:741d9540 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:741d9540 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 1#67 16564936 Illumina sequencing of library 16564936 constructed from sample accession ERS1079216 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 1. This submission includes reads tagged with the sequence TACCACCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_1#67.cram cram 332077800.0 1660389.0 SC RUN 19850 1#67 0:100 1:100 A:88958890;C:76946124;G:77079866;T:89022508;N:70412 100 100     88958890 76946124 77079866 89022508 70412 ERX1513004 ERS1079216 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96162 0.96369 0.11367 0.11586 0.7992 0.79855 0.58505 0.58088 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
4062 4062 ERR1442626 ERX1513003 ERS1079215 ERP014517 PRJEB12982 Baseline expression from transcriptional profiling of zebrafish developmental stages 3 Baseline_expression_from_transcriptional_profiling_of_zebrafish_developmental_stages_3-sc-4130 Transcriptome Analysis RNA Seq data was generated from RNA of wild type zebrafish embryo pools at different stages of development for baseline transcriptional profiling ArrayExpress:E ERAD 475     ZMP phenotype 128 B SAMEA3892081 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:Cleavage:2 cell ZFS:0000002|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 06 06|ENA last update:2016 03 10|External Id:SAMEA3892081|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 06 06T15:24:12Z|INSDC last update:2016 03 10T13:38:05Z|INSDC status:public|Submitter Id:74118750 e60c 11e5 bc69 3c4a9275d6c6|common name:zebrafish|sample description:RNA from a pool of 12 single wild type zebrafish embryos plus ERCC spike mix 2 Ambion. The sample has been DNAse treated.|sample name:74118750 e60c 11e5 bc69 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 paired end sequencing SC EXP 19850 1#66 16564924 Illumina sequencing of library 16564924 constructed from sample accession ERS1079215 for study accession ERP014517. This is part of an Illumina multiplexed sequencing run 19850 1. This submission includes reads tagged with the sequence TGAAGCCA. RNA seq dUTP eukaryotic   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   ERP014517 Illumina HiSeq 2500 paired end sequencing ENA FIRST PUBLIC:2016 06 06|ENA LAST UPDATE:2018 11 16 19850_1#66.cram cram 332776400.0 1663882.0 SC RUN 19850 1#66 0:100 1:100 A:88108657;C:78400833;G:78371292;T:87823689;N:71929 100 100     88108657 78400833 78371292 87823689 71929 ERX1513003 ERS1079215 ERA648700 European Nucleotide Archive Wellcome Sanger Institute 2 0.96154 0.96535 0.12909 0.13161 0.79815 0.79959 0.58756 0.58417 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2016-03-10 Cleavage Embryo Whole Organism All anatomical structures
9296 9296 ERR202508 ERX177193 ERS092407 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570569 SC ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:T/LF|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:29Z|External Id:SAMEA1570569|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:29Z|INSDC status:public|Submitter Id:2C TotRNA sc 2012 02 06T13:12:17Z 1121923|common name:zebrafish|sample description:RNA seq|sample name:2C TotRNA sc 2012 02 06T13:12:17Z 1121923|scientific name:Danio rerio|strain:T/LF                 1 SC EXP 6683 2 2532385 Illumina sequencing of library 2532385 constructed from sample accession ERS092407 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001280 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 6683_2.bam bam 11463941550.0 76426277.0 SC RUN 6683 2 0:75 1:75 A:2384324967;C:3291391074;G:3291238330;T:2457078635;N:39908544 75 75     2384324967 3291391074 3291238330 2457078635 39908544 ERX177193 ERS092407 ERA176708 SC Wellcome Sanger Institute 2 0.96484 0.95918 0.35968 0.35526 0.88404 0.88485 0.84949 0.8524 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
9298 9298 ERR202506 ERX177191 ERS092405 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570534 SC ArrayExpress DevelopmentalStage:16 cell|ArrayExpress Genotype:T/LF|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Sex:mixed|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:25Z|External Id:SAMEA1570534|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:25Z|INSDC status:public|Submitter Id:16C stan pro sc 2012 02 06T13:12:14Z 1121921|common name:zebrafish|sample description:RNA seq|sample name:16C stan pro sc 2012 02 06T13:12:14Z 1121921|scientific name:Danio rerio|strain:T/LF                 1 SC EXP 6317 5 2532383 Illumina sequencing of library 2532383 constructed from sample accession ERS092405 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   ERP001280 Illumina HiSeq 2000 paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 6317_5.bam bam 7092438300.0 47282922.0 SC RUN 6317 5 0:75 1:75 A:1947926886;C:1582039071;G:1595096528;T:1959471222;N:7904593 75 75     1947926886 1582039071 1595096528 1959471222 7904593 ERX177191 ERS092405 ERA176708 SC Wellcome Sanger Institute 2 0.90801 0.90631 0.0426 0.04216 0.78486 0.78539 0.4795 0.47872 75 75 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
9301 9301 ERR202503 ERX177188 ERS092094 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570566 SC ArrayExpress DevelopmentalStage:64 cell|ArrayExpress Genotype:SAT/WIK|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:31Z|External Id:SAMEA1570566|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:31Z|INSDC status:public|Submitter Id:SAT b sc 2012 02 06T13:05:45Z 998060|common name:zebrafish|sample description:RNA seq|sample name:SAT b sc 2012 02 06T13:05:45Z 998060|scientific name:Danio rerio|strain:SAT                 1 SC EXP 5552 6 1476240 Illumina sequencing of library 1476240 constructed from sample accession ERS092094 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001280 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 5552_6.bam bam 3031861428.0 28072791.0 SC RUN 5552 6 0:54 1:54 A:827548202;C:685397282;G:689217947;T:827560833;N:2137164 54 54     827548202 685397282 689217947 827560833 2137164 ERX177188 ERS092094 ERA176708 SC Wellcome Sanger Institute 2 0.88709 0.8867 0.04219 0.04381 0.76836 0.76978 0.48688 0.48607 54 54 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
9304 9304 ERR202500 ERX177185 ERS092093 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570541 SC ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:SAT/WIK|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:13Z|External Id:SAMEA1570541|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:13Z|INSDC status:public|Submitter Id:SAT a sc 2012 02 06T13:05:43Z 998059|common name:zebrafish|sample description:RNA seq|sample name:SAT a sc 2012 02 06T13:05:43Z 998059|scientific name:Danio rerio|strain:SAT                 1 SC EXP 5540 7 1392795 Illumina sequencing of library 1392795 constructed from sample accession ERS092093 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001280 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 5540_7.bam bam 4139896608.0 38332376.0 SC RUN 5540 7 0:54 1:54 A:1123995667;C:935834208;G:933659183;T:1138309303;N:8098247 54 54     1123995667 935834208 933659183 1138309303 8098247 ERX177185 ERS092093 ERA176708 SC Wellcome Sanger Institute 2 0.89473 0.89261 0.0475 0.0496 0.80413 0.80551 0.49672 0.49064 54 54 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
9308 9308 ERR202496 ERX177181 ERS092089 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570537 SC ArrayExpress DevelopmentalStage:64 cell|ArrayExpress Genotype:WIK/SAT|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:15Z|External Id:SAMEA1570537|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:15Z|INSDC status:public|Submitter Id:WIK b sc 2012 02 06T13:05:39Z 998055|common name:zebrafish|sample description:RNA seq|sample name:WIK b sc 2012 02 06T13:05:39Z 998055|scientific name:Danio rerio|strain:WIK                 1 SC EXP 5540 2 1392791 Illumina sequencing of library 1392791 constructed from sample accession ERS092089 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001280 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 5540_2.bam bam 3934066536.0 36426542.0 SC RUN 5540 2 0:54 1:54 A:1089272408;C:875257818;G:871131618;T:1090449345;N:7955347 54 54     1089272408 875257818 871131618 1090449345 7955347 ERX177181 ERS092089 ERA176708 SC Wellcome Sanger Institute 2 0.92002 0.92014 0.04875 0.05104 0.76061 0.76161 0.4821 0.48296 54 54 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
9309 9309 ERR202495 ERX177180 ERS092088 ERP001280 PRJEB2925 maternal to Zygotic Transition maternal_to_Zygotic_Transition-sc-2012-03-12T11:38:43Z-599 Transcriptome Analysis During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development known as the maternal to zygotic transition MZT the genome becomes activated and the maternally provided mRNAs begin to degrade. We plan to map the mRNA profiles of genes during the maternal to zygotic transition by using solexa sequencing.         SAMEA1570572 SC ArrayExpress DevelopmentalStage:2 cell|ArrayExpress Genotype:WIK/SAT|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Phenotype:WT|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2012 11 28T14:59:05Z|ENA LAST UPDATE:2018 03 08T15:36:31Z|External Id:SAMEA1570572|INSDC center name:SC|INSDC first public:2012 11 28T14:59:05Z|INSDC last update:2018 03 08T15:36:31Z|INSDC status:public|Submitter Id:WIK a sc 2012 02 06T13:05:37Z 998054|common name:zebrafish|sample description:RNA seq|sample name:WIK a sc 2012 02 06T13:05:37Z 998054|scientific name:Danio rerio|strain:WIK                 1 SC EXP 5540 1 1392790 Illumina sequencing of library 1392790 constructed from sample accession ERS092088 for study accession ERP001280. Illumina cDNA protocol   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina Genome Analyzer II   ERP001280 Illumina Genome Analyzer II paired end sequencing ENA FIRST PUBLIC:2012 11 28|ENA LAST UPDATE:2018 11 16 5540_1.bam bam 4120158204.0 38149613.0 SC RUN 5540 1 0:54 1:54 A:1165514767;C:896704109;G:892695229;T:1156428740;N:8815359 54 54     1165514767 896704109 892695229 1156428740 8815359 ERX177180 ERS092088 ERA176708 SC Wellcome Sanger Institute 2 0.9228 0.92241 0.05498 0.05795 0.79091 0.79235 0.50034 0.50151 54 54 B B biological fallback assumption illumina early_illumina unknown cdna_unspecified unknown bulk unknown unknown   United Kingdom 2012-11-28 Cleavage Embryo Whole Organism All anatomical structures
29229 29229 SRR27489746 SRX23160963 SRS20111121 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica C MPRA repC fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica C Library 36 Library 36 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz fastq fastq 13085558528.0 43329664.0 BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985 151 151     3305413622 3391845548 3249932870 3137708503 657985 SRX23160963 SRS20111121 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01098 8e-05 0.00025 0.0 0.99216 0.99973 0.4317 0.61538 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29230 29230 SRR27489747 SRX23160962 SRS20111119 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica C MPRA repC fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica C Library 35 Library 35 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz fastq fastq 16647721914.0 55124907.0 BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108 151 151     4231542934 4348688006 4050131444 4016534422 825108 SRX23160962 SRS20111119 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01514 0.00017 0.00035 3e-05 0.99109 0.99955 0.4372 0.30434 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29231 29231 SRR27489748 SRX23160961 SRS20111118 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica C MPRA repC fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica C Library 34 Library 34 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz fastq fastq 15431181052.0 51096626.0 BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999 151 151     3856018869 4036338306 3877988553 3660059325 775999 SRX23160961 SRS20111118 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01114 8e-05 0.00028 0.0 0.99192 0.99975 0.42956 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29232 29232 SRR27489749 SRX23160960 SRS20111117 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica C MPRA repC input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 2hpf replica C Library 33 Library 33 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz fastq fastq 11771229160.0 38977580.0 BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080 151 151     2999574420 3115525474 2806539264 2849003922 586080 SRX23160960 SRS20111117 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01997 2e-05 0.00054 0.0 0.99022 0.99993 0.41853 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29235 29235 SRR27489752 SRX23160957 SRS20111114 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica A MPRA repA fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica A Library 4 Library 4 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz fastq fastq 12108626278.0 40094789.0 BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268 151 151     3079403604 3149095123 2953175005 2926352278 600268 SRX23160957 SRS20111114 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.014 5e-05 0.00032 0.0 0.99137 0.99987 0.45127 0.28571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29246 29246 SRR27489763 SRX23160946 SRS20111108 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica A MPRA repA fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica A Library 3 Library 3 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz fastq fastq 12524202136.0 41470868.0 BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842 151 151     3168466372 3269998328 3075956662 3009160932 619842 SRX23160946 SRS20111108 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01351 7e-05 0.00028 0.0 0.99168 0.99977 0.43472 0.54545 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29247 29247 SRR27489764 SRX23160945 SRS20111103 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica B MPRA repB fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica B Library 20 Library 20 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz fastq fastq 12514444214.0 41438557.0 BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303 151 151     3174354240 3246812350 3082021359 3010633962 622303 SRX23160945 SRS20111103 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01121 0.00016 0.00027 1e-05 0.99204 0.99953 0.43533 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29248 29248 SRR27489765 SRX23160944 SRS20111102 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica B MPRA repB fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica B Library 19 Library 19 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz fastq fastq 16535129670.0 54752085.0 BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421 151 151     4184643114 4312135767 4051628900 3985895468 826421 SRX23160944 SRS20111102 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01416 0.00017 0.00031 1e-05 0.9917 0.99941 0.40732 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29249 29249 SRR27489766 SRX23160943 SRS20111101 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica B MPRA repB fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica B Library 18 Library 18 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz fastq fastq 12692870042.0 42029371.0 BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284 151 151     3179006274 3325152682 3173386021 3014687781 637284 SRX23160943 SRS20111101 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01199 8e-05 0.0003 1e-05 0.99145 0.99979 0.40897 0.36363 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29250 29250 SRR27489767 SRX23160942 SRS20111100 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica B MPRA repB input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 2hpf replica B Library 17 Library 17 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz fastq fastq 13169436008.0 43607404.0 BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755 151 151     3341908647 3485072739 3171200836 3170595031 658755 SRX23160942 SRS20111100 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01868 5e-05 0.0006 0.0 0.99038 0.99983 0.41955 0.125 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29257 29257 SRR27489774 SRX23160935 SRS20111093 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica A MPRA repA fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica A Library 2 Library 2 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz fastq fastq 16111078182.0 53347941.0 BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034 151 151     4069536779 4222816450 3957789955 3860129964 805034 SRX23160935 SRS20111093 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01511 5e-05 0.00034 0.0 0.99135 0.99985 0.41564 0.42857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29258 29258 SRR27489775 SRX23160934 SRS20111092 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica A MPRA repA input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 2hpf replica A Library 1 Library 1 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz fastq fastq 9769305890.0 32348695.0 BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485 151 151     2477269774 2598109179 2338444856 2354997596 484485 SRX23160934 SRS20111092 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0205 4e-05 0.00059 0.0 0.99013 0.99987 0.41957 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29718 29718 SRR27485663 SRX23156886 SRS20107307 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell R3   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:3|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: embryo 1 hpf rep4 EV06010 EV06010 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     EV06010.R1.fastq.gz fastq 620142356.0 8227837.0 EV06010.R1.fastq.gz 0:75.37 A:186029536;C:118842640;G:134072972;T:181171903;N:25305 75       186029536 118842640 134072972 181171903 25305 SRX23156886 SRS20107307 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.90656   0.06918   0.80192   0.72472   76   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29725 29725 SRR27485670 SRX23156879 SRS20107300 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:2|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: embryo 1 hpf rep4 EV06003 EV06003 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     EV06003.R1.fastq.gz fastq 706095550.0 9366364.0 EV06003.R1.fastq.gz 0:75.39 A:204324355;C:140058731;G:159377323;T:202282197;N:52944 75       204324355 140058731 159377323 202282197 52944 SRX23156879 SRS20107300 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.90788   0.10297   0.80168   0.71073   76   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29736 29736 SRR27477296 SRX23148651 SRS20099370 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|replicate:4|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: embryo 1 hpf rep4 EV09003 EV09003 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     EV09003.R1.fastq.gz fastq 438955973.0 5837128.0 EV09003.R1.fastq.gz 0:75.20 A:134628611;C:87460856;G:98199538;T:118638244;N:28724 75       134628611 87460856 98199538 118638244 28724 SRX23148651 SRS20099370 SRA1782413 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.89029   0.11994   0.80833   0.72581   76   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-10 Cleavage Embryo Whole Organism All anatomical structures
29743 29743 SRR27467676 SRX23139230 SRS20090273 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep2 EV04004 EV04004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04004.R1.fastq.gz fastq 895671560.0 6397654.0 EV04004.R1.fastq.gz 0:140 A:206443066;C:147067097;G:365386937;T:176734600;N:39860 140       206443066 147067097 365386937 176734600 39860 SRX23139230 SRS20090273 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.0   0.0   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29744 29744 SRR27467677 SRX23139229 SRS20090274 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep2 EV04003 EV04003 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV04003.R1.fastq.gz fastq 664112120.0 4743658.0 EV04003.R1.fastq.gz 0:140 A:163711695;C:142612940;G:211194350;T:146562626;N:30509 140       163711695 142612940 211194350 146562626 30509 SRX23139229 SRS20090274 SRA1781872 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-09 Cleavage Embryo Whole Organism All anatomical structures
29758 29758 SRR27437478 SRX23109819 SRS20064573 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep3 EV07006 EV07006 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07006.R1.fastq.gz fastq 2584527680.0 18460912.0 EV07006.R1.fastq.gz 0:140 A:685107500;C:367766834;G:717359848;T:814224206;N:69292 140       685107500 367766834 717359848 814224206 69292 SRX23109819 SRS20064573 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 2e-05   1e-05   1.0       140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29759 29759 SRR27437479 SRX23109818 SRS20064571 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep3 EV07005 EV07005 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07005.R1.fastq.gz fastq 713829480.0 5098782.0 EV07005.R1.fastq.gz 0:140 A:183575304;C:168886779;G:213156258;T:148191838;N:19301 140       183575304 168886779 213156258 148191838 19301 SRX23109818 SRS20064571 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 5e-05   0.0   0.99989   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29760 29760 SRR27437480 SRX23109817 SRS20064572 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R3   strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep3 EV07004 EV07004 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV07004.R1.fastq.gz fastq 517336680.0 3695262.0 EV07004.R1.fastq.gz 0:140 A:136783049;C:131207858;G:139873280;T:109458276;N:14217 140       136783049 131207858 139873280 109458276 14217 SRX23109817 SRS20064572 SRA1780298 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 7e-05   0.0   0.99981   0.7   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-06 Cleavage Embryo Whole Organism All anatomical structures
29779 29779 SRR27435864 SRX23108232 SRS20063068 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell BS R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:BS|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf BS rep4 EV08009 EV08009 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08009.R1.fastq.gz fastq 756964460.0 5406889.0 EV08009.R1.fastq.gz 0:140 A:191381054;C:111783194;G:185694475;T:268052883;N:52854 140       191381054 111783194 185694475 268052883 52854 SRX23108232 SRS20063068 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 1e-05   0.0   0.99997   1.0   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29780 29780 SRR27435865 SRX23108231 SRS20063069 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell DM R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:DM|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf DM rep4 EV08008 EV08008 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08008.R1.fastq.gz fastq 751794680.0 5369962.0 EV08008.R1.fastq.gz 0:140 A:194845808;C:197389162;G:194749636;T:164756481;N:53593 140       194845808 197389162 194749636 164756481 53593 SRX23108231 SRS20063069 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00124   0.00029   0.99853   0.77083   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
29781 29781 SRR27435866 SRX23108230 SRS20063066 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           4 cell mock R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:1 hpf|collection date:2022|geo loc name:Austria|sex:mixed|tissue:whole embryo|treatment:mock|BioSampleModel:Model organism or animal                 tRAM seq of zebrafish: embryo 1 hpf mock rep4 EV08007 EV08007 RNA was extracted with Trizol tRNA isolated by size selection on denaturing polyacrylamide gel range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment three prime adapter ligated with T4 RNA ligase 2 reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase using NEB Next indexed primers.     OTHER TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA NextSeq 500   SRP482074     EV08007.R1.fastq.gz fastq 761961760.0 5442584.0 EV08007.R1.fastq.gz 0:140 A:194053323;C:191169414;G:194452160;T:182234253;N:52610 140       194053323 191169414 194452160 182234253 52610 SRX23108230 SRS20063066 SRA1780265 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.00242   0.00062   0.99803   0.81818   140   T   under 1.2% mapping rate illumina nextseq unknown size_fractionation nebnext bulk unknown unknown   Austria 2024-01-05 Cleavage Embryo Whole Organism All anatomical structures
30769 30769 SRR28348935 SRX23954961 SRS20755382 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Embryo 2hpf rep3 GSM8147858   source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Embryo 2hpf rep3 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Whole embryo   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF GSM8147858 GSM8147858: Zebrafish Embryo 2hpf rep3; Danio rerio; RNA Seq GSM8147858 r1 GSM8147858 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     s_2hpf_3.fastq fastq 1748504032.0 23006632.0 GSM8147858 r1 0:76 A:420580006;C:434589498;G:408972977;T:484281127;N:80424 76       420580006 434589498 408972977 484281127 80424 SRX23954961 SRS20755382 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Cleavage Embryo Whole Organism All anatomical structures
30770 30770 SRR28348936 SRX23954960 SRS20755381 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Embryo 2hpf rep2 GSM8147857   source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Embryo 2hpf rep2 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Whole embryo   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF GSM8147857 GSM8147857: Zebrafish Embryo 2hpf rep2; Danio rerio; RNA Seq GSM8147857 r1 GSM8147857 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     s_2hpf_2.fastq fastq 1578919456.0 20775256.0 GSM8147857 r1 0:76 A:380440230;C:393721925;G:368114931;T:436571104;N:71266 76       380440230 393721925 368114931 436571104 71266 SRX23954960 SRS20755381 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Cleavage Embryo Whole Organism All anatomical structures
30771 30771 SRR28348937 SRX23954959 SRS20755380 SRP495323 PRJNA1088158 Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. GSE261646 Transcriptome Analysis The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…   pubmed:39302832   Zebrafish Embryo 2hpf rep1 GSM8147856   source name:Whole embryo|tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF|geo loc name:missing|collection date:missing Zebrafish Embryo 2hpf rep1 Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates Whole embryo   Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   tissue:Whole embryo|developmental stage:2hpf|genotype:AB TF and TLF GSM8147856 GSM8147856: Zebrafish Embryo 2hpf rep1; Danio rerio; RNA Seq GSM8147856 r1 GSM8147856 1 Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP495323     s_2hpf_1.fastq fastq 1730435412.0 22768887.0 GSM8147856 r1 0:76 A:420026952;C:428388301;G:403718608;T:478219805;N:81746 76       420026952 428388301 403718608 478219805 81746 SRX23954959 SRS20755380 SRA1824599 Computational Biology, Stowers Institute for Medical Research Computational Biology, Stowers Institute for Medical Research                       B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk bulk bulk   United States 2024-03-14 Cleavage Embryo Whole Organism All anatomical structures
32033 32033 SRR28976522 SRX24505963 SRS21254128 SRP506702 PRJNA1109723 rbm24a is an organizer component of germ plasm to determine germ cell fate GSE267086 Other The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.       Zebrafish RIP seq Rbm24a Knock in IP GSM8259538   source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing Zebrafish RIP seq Rbm24a Knock in IP Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP GSM8259538 GSM8259538: Zebrafish RIP seq Rbm24a Knock in IP; Danio rerio; RIP Seq GSM8259538 r1 GSM8259538 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506702     RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz fastq fastq 6457893104.0 21383752.0 GSM8259538 r1 0:151 1:151 A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968 151 151     975588225 2019180290 2469634919 992947702 541968 SRX24505963 SRS21254128 SRA1863578 Ang Li, College of Life Sciences, shandong university Ang Li, College of Life Sciences, shandong university 2 0.90304 0.86018 0.20083 0.20471 0.96382 0.96743 0.96102 0.98876 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   China 2024-05-09 Cleavage Embryo Whole Organism All anatomical structures
32034 32034 SRR28976523 SRX24505962 SRS21254127 SRP506702 PRJNA1109723 rbm24a is an organizer component of germ plasm to determine germ cell fate GSE267086 Other The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.       Zebrafish RIP seq wild type IP GSM8259537   source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing Zebrafish RIP seq wild type IP Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP GSM8259537 GSM8259537: Zebrafish RIP seq wild type IP; Danio rerio; RIP Seq GSM8259537 r1 GSM8259537 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506702     RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz fastq fastq 4501412680.0 14905340.0 GSM8259537 r1 0:151 1:151 A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621 151 151     651609366 1285679784 1901211768 662533141 378621 SRX24505962 SRS21254127 SRA1863578 Ang Li, College of Life Sciences, shandong university Ang Li, College of Life Sciences, shandong university 2 0.96426 0.81361 0.26579 0.2253 0.97784 0.97806 0.8699 0.93379 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   China 2024-05-09 Cleavage Embryo Whole Organism All anatomical structures
32035 32035 SRR28976524 SRX24505961 SRS21254126 SRP506702 PRJNA1109723 rbm24a is an organizer component of germ plasm to determine germ cell fate GSE267086 Other The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.       Zebrafish RIP seq Rbm24a Knock in input GSM8259536   source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing Zebrafish RIP seq Rbm24a Knock in input Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input GSM8259536 GSM8259536: Zebrafish RIP seq Rbm24a Knock in input; Danio rerio; RIP Seq GSM8259536 r1 GSM8259536 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506702     RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz fastq fastq 9539398726.0 31587413.0 GSM8259536 r1 0:151 1:151 A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896 151 151     2233069830 2078359171 3009942870 2217201959 824896 SRX24505961 SRS21254126 SRA1863578 Ang Li, College of Life Sciences, shandong university Ang Li, College of Life Sciences, shandong university 2 0.90112 0.81448 0.02415 0.01993 0.79287 0.79807 0.47884 0.48186 151 151 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk bulk bulk   China 2024-05-09 Cleavage Embryo Whole Organism All anatomical structures
32036 32036 SRR28976525 SRX24505960 SRS21254125 SRP506702 PRJNA1109723 rbm24a is an organizer component of germ plasm to determine germ cell fate GSE267086 Other The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.       Zebrafish RIP seq wild type input GSM8259535   source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing Zebrafish RIP seq wild type input Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input GSM8259535 GSM8259535: Zebrafish RIP seq wild type input; Danio rerio; RIP Seq GSM8259535 r1 GSM8259535 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RIP-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina NovaSeq 6000   SRP506702     RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz fastq fastq 14180410302.0 46955001.0 GSM8259535 r1 0:151 1:151 A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400 151 151     3380011534 2883841476 4593876270 3321465622 1215400 SRX24505960 SRS21254125 SRA1863578 Ang Li, College of Life Sciences, shandong university Ang Li, College of Life Sciences, shandong university 2 0.86497 0.64685 0.04432 0.02854 0.79324 0.8031 0.52927 0.53304 151 151 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk bulk bulk   China 2024-05-09 Cleavage Embryo Whole Organism All anatomical structures
34036 34036 SRR31033345 SRX26418807 SRS22938440 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish Riboseq M 4cell 5 GSM8579730   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing Zebrafish Riboseq M 4cell 5 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a GSM8579730 GSM8579730: Zebrafish Riboseq M 4cell 5; Danio rerio; RNA Seq GSM8579730 r1 GSM8579730 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     M-4cell-5_L1_1.fq.gz M-4cell-5_L1_2.fq.gz fastq fastq 5643278100.0 18810927.0 GSM8579730 r1 0:150 1:150 A:1555401034;C:1268722567;G:1323837426;T:1495279385;N:37688 150 150     1555401034 1268722567 1323837426 1495279385 37688 SRX26418807 SRS22938440 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34037 34037 SRR31033351 SRX26418806 SRS22938443 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish Riboseq M 4cell 4 GSM8579729   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing Zebrafish Riboseq M 4cell 4 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a GSM8579729 GSM8579729: Zebrafish Riboseq M 4cell 4; Danio rerio; RNA Seq GSM8579729 r1 GSM8579729 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     M-4cell-4_L1_1.fq.gz M-4cell-4_L1_2.fq.gz fastq fastq 6607232100.0 22024107.0 GSM8579729 r1 0:150 1:150 A:1825603885;C:1480833466;G:1538474482;T:1762276005;N:44262 150 150     1825603885 1480833466 1538474482 1762276005 44262 SRX26418806 SRS22938443 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34038 34038 SRR31033346 SRX26418805 SRS22938438 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish Riboseq M 4cell 3 GSM8579728   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing Zebrafish Riboseq M 4cell 3 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a GSM8579728 GSM8579728: Zebrafish Riboseq M 4cell 3; Danio rerio; RNA Seq GSM8579728 r1 GSM8579728 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     M-4cell-3_L1_1.fq.gz M-4cell-3_L1_2.fq.gz fastq fastq 7948794900.0 26495983.0 GSM8579728 r1 0:150 1:150 A:2183592013;C:1794605656;G:1863773539;T:2106770087;N:53605 150 150     2183592013 1794605656 1863773539 2106770087 53605 SRX26418805 SRS22938438 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34039 34039 SRR31033350 SRX26418804 SRS22938441 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish Riboseq M 4cell 2 GSM8579727   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a|geo loc name:missing|collection date:missing Zebrafish Riboseq M 4cell 2 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:Mrbm24a GSM8579727 GSM8579727: Zebrafish Riboseq M 4cell 2; Danio rerio; RNA Seq GSM8579727 r1 GSM8579727 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     M-4cell-2_L1_1.fq.gz M-4cell-2_L1_2.fq.gz fastq fastq 7036510200.0 23455034.0 GSM8579727 r1 0:150 1:150 A:1830698676;C:1686461802;G:1754202163;T:1765099649;N:47910 150 150     1830698676 1686461802 1754202163 1765099649 47910 SRX26418804 SRS22938441 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34047 34047 SRR31033355 SRX26418796 SRS22938428 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish RNAseq Sibling 4cell 4 GSM8579719   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing Zebrafish RNAseq Sibling 4cell 4 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type GSM8579719 GSM8579719: Zebrafish RNAseq Sibling 4cell 4; Danio rerio; RNA Seq GSM8579719 r1 GSM8579719 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     Sibling-4cell-4_L1_1.fq.gz Sibling-4cell-4_L1_2.fq.gz fastq fastq 7424662500.0 24748875.0 GSM8579719 r1 0:150 1:150 A:2045351766;C:1671617139;G:1731338149;T:1976305596;N:49850 150 150     2045351766 1671617139 1731338149 1976305596 49850 SRX26418796 SRS22938428 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34048 34048 SRR31033358 SRX26418795 SRS22938431 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish RNAseq Sibling 4cell 2 GSM8579718   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing Zebrafish RNAseq Sibling 4cell 2 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type GSM8579718 GSM8579718: Zebrafish RNAseq Sibling 4cell 2; Danio rerio; RNA Seq GSM8579718 r1 GSM8579718 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     Sibling-4cell-2_L1_1.fq.gz Sibling-4cell-2_L1_2.fq.gz fastq fastq 6484454400.0 21614848.0 GSM8579718 r1 0:150 1:150 A:1701212104;C:1544478776;G:1597991536;T:1640728663;N:43321 150 150     1701212104 1544478776 1597991536 1640728663 43321 SRX26418795 SRS22938431 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
34049 34049 SRR31033356 SRX26418794 SRS22938430 SRP539223 PRJNA1174207 Rbm24 dictates mRNA recruitment for germ plasm assembly GSE279756 Transcriptome Analysis Ribonucleoprotein RNP granules are the most common membrane less biomolecular condensates. However the mechanisms underlying their assembly are largely unknown. The aggregation of germ plasm determines the fate of primordial germ cells PGCs and serves as a model for RNP granule assembly. Here we show that maternal RNA binding protein Rbm24a is the key factor governing specific sorting of mRNAs. Mechanistically Rbm24a complexes with Buc and interacts to dictate the specific grasp of germ plasm mRNAs into phase separated condensates. Germ plasm particles lacking Rbm24a and mRNAs fail to undergo kinesin dependent transport towards the cleavage furrows where small granules fuse into large aggregates. Therefore the loss of maternal Rbm24a causes a complete degradation of germ plasm and the disappearance of PGCs. These findings demonstrate that Rbm24a functions as a nucleating organizer of the germ plasm highlighting an emerging mechanism for RNA binding proteins in reading and recruiting RNA components into the phase separated protein scaffold. Overall design: To examine the global transcriptome alterations following the loss of maternal Rbm24a we conducted bulk RNA seq analysis on Mrbm24a and their sibling embyos at 4 cell sphere stage and 24 hpf.       Zebrafish RNAseq Sibling 4cell 1 GSM8579717   source name:whole embryo|tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type|geo loc name:missing|collection date:missing Zebrafish RNAseq Sibling 4cell 1 Each library was amplified by a 11 cycle PCR and 150 bp paired end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: tab delimited text file includes FPKM values for each Sample whole embryo   Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions. Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C tissue:whole embryo|Stage:4 cell stage|cell type:embryonic cell|genotype:wild type GSM8579717 GSM8579717: Zebrafish RNAseq Sibling 4cell 1; Danio rerio; RNA Seq GSM8579717 r1 GSM8579717 1 Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP539223     Sibling-4cell-1_L1_1.fq.gz Sibling-4cell-1_L1_2.fq.gz fastq fastq 8126999700.0 27089999.0 GSM8579717 r1 0:150 1:150 A:2195769442;C:1872416059;G:1934390760;T:2124367874;N:55565 150 150     2195769442 1872416059 1934390760 2124367874 55565 SRX26418794 SRS22938430 SRA1993092 Shandong university Shandong university                       B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk bulk bulk   China 2024-10-17 Cleavage Embryo Whole Organism All anatomical structures
36297 36297 SRR393000 SRX113357 SRS284301 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments Wild type 2hpf 2 GSM854439   source name:Whole embryo wild type|sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|development stage:2hpf Ribosome protected fragments Wild type 2hpf 2 Ribo Wt 2 B.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo wild type   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|developmental stage:2hpf GSM854439 GSM854439: Ribosome protected fragments Wild type 2hpf 2; Danio rerio; RNA Seq GSM854439 1 GSM854439: Ribosome protected fragments Wild type 2hpf 2 1   GEO Accession:GSM854439 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040     Ribo_Wt_2_B1.fq fastq 217015848.0 3014109.0 GSM854439 r1 0:72 A:73500339;C:46583724;G:47804114;T:49117423;N:10248 72       73500339 46583724 47804114 49117423 10248 SRX113357 SRS284301 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 2e-05   0.0   0.99997   1.0   72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36298 36298 SRR393001 SRX113357 SRS284301 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments Wild type 2hpf 2 GSM854439   source name:Whole embryo wild type|sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|development stage:2hpf Ribosome protected fragments Wild type 2hpf 2 Ribo Wt 2 B.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo wild type   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|developmental stage:2hpf GSM854439 GSM854439: Ribosome protected fragments Wild type 2hpf 2; Danio rerio; RNA Seq GSM854439 1 GSM854439: Ribosome protected fragments Wild type 2hpf 2 1   GEO Accession:GSM854439 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040   instrument model:Illumina HiSeq 2000 Ribo_Wt_2_B2.fq fastq 976804848.0 13566734.0 GSM854439 r2 0:72 A:312362919;C:205660950;G:237663406;T:221097191;N:20382 72       312362919 205660950 237663406 221097191 20382 SRX113357 SRS284301 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 0.0   0.0   1.0       72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36299 36299 SRR392998 SRX113356 SRS284300 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments Wild type 2hpf GSM854438   source name:Whole embryo wild type|sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|development stage:2hpf Ribosome protected fragments Wild type 2hpf Ribo Wt 2 A.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo wild type   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|developmental stage:2hpf GSM854438 GSM854438: Ribosome protected fragments Wild type 2hpf; Danio rerio; RNA Seq GSM854438 1 GSM854438: Ribosome protected fragments Wild type 2hpf 1   GEO Accession:GSM854438 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040     Ribo_Wt_2_A1.fq fastq 284876712.0 3956621.0 GSM854438 r1 0:72 A:88022040;C:68867093;G:63794882;T:64180749;N:11948 72       88022040 68867093 63794882 64180749 11948 SRX113356 SRS284300 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 0.00011   7e-05   0.99995   0.0   72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36300 36300 SRR392999 SRX113356 SRS284300 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments Wild type 2hpf GSM854438   source name:Whole embryo wild type|sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|development stage:2hpf Ribosome protected fragments Wild type 2hpf Ribo Wt 2 A.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo wild type   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:wild type|developmental stage:2hpf GSM854438 GSM854438: Ribosome protected fragments Wild type 2hpf; Danio rerio; RNA Seq GSM854438 1 GSM854438: Ribosome protected fragments Wild type 2hpf 1   GEO Accession:GSM854438 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040   instrument model:Illumina HiSeq 2000 Ribo_Wt_2_A2.fq fastq 1197987552.0 16638716.0 GSM854438 r2 0:72 A:346631182;C:288138913;G:296030268;T:267150788;N:36401 72       346631182 288138913 296030268 267150788 36401 SRX113356 SRS284300 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 3e-05   0.0   0.99997   0.0   72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36309 36309 SRR392988 SRX113351 SRS284295 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments MZdicer 2hpf 2 GSM854433   source name:Whole embryo MZdicer|sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|development stage:2hpf Ribosome protected fragments MZdicer 2hpf 2 Ribo Dicer 2 B.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo MZdicer   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|developmental stage:2hpf GSM854433 GSM854433: Ribosome protected fragments MZdicer 2hpf 2; Danio rerio; RNA Seq GSM854433 1 GSM854433: Ribosome protected fragments MZdicer 2hpf 2 1   GEO Accession:GSM854433 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040     Ribo_Dicer_2_B1.fq fastq 72956952.0 1013291.0 GSM854433 r1 0:72 A:22006501;C:17986138;G:16833834;T:16127785;N:2694 72       22006501 17986138 16833834 16127785 2694 SRX113351 SRS284295 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 0.00131   0.00114   0.99991   0.88888   72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36310 36310 SRR392989 SRX113351 SRS284295 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments MZdicer 2hpf 2 GSM854433   source name:Whole embryo MZdicer|sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|development stage:2hpf Ribosome protected fragments MZdicer 2hpf 2 Ribo Dicer 2 B.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo MZdicer   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|developmental stage:2hpf GSM854433 GSM854433: Ribosome protected fragments MZdicer 2hpf 2; Danio rerio; RNA Seq GSM854433 1 GSM854433: Ribosome protected fragments MZdicer 2hpf 2 1   GEO Accession:GSM854433 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040   instrument model:Illumina HiSeq 2000 Ribo_Dicer_2_B2.fq fastq 454127328.0 6307324.0 GSM854433 r2 0:72 A:124676855;C:112665084;G:119208313;T:97572172;N:4904 72       124676855 112665084 119208313 97572172 4904 SRX113351 SRS284295 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 0.0   0.0   1.0       72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures
36311 36311 SRR392986 SRX113350 SRS284294 SRP010040 PRJNA150397 Ribosome profiling of early zebrafish embryos miRNA mediated regulation during embryogenesis causes translational repression before mRNA decay GSE34743 Transcriptome Analysis MicroRNAs regulate gene expression through deadenylation repression and mRNA decay. However the contribution of each mechanism in non steady state situations remains unclear. We monitored the impact of miR 430 on ribosome occupancy of endogenous mRNAs in wild type and dicer mutants lacking mature miR 430. Our results indicate that miR 430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation and disrupting deadenylation using an internal polyA tail did not block target repression. Finally we observe that ribosome density along the length of the target mRNA remains constant suggesting that translational repression occurs by reducing the initiation rate rather than reducing elongation or causing ribosomal drop off. In summary our results show that miR 430 regulates translation initiation before inducing mRNA decay. Overall design: Time course parallel ribosome profiling and input mRNA quantification in wildtype and MZdicer mutant embryos   pubmed:22422859   Ribosome protected fragments MZdicer 2hpf GSM854432   source name:Whole embryo MZdicer|sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|development stage:2hpf Ribosome protected fragments MZdicer 2hpf Ribo Dicer 2 A.bed; genome build: danRer7 Tophat v1.2.0 alignment to UCSC danRer7 Zv9 genome sequence guided by Ensembl r63 gene models; default settings limited to reads mapping 5 or fewer times. Reads were trimmed of three prime adapter sequence Whole embryo MZdicer   Ribosome protected fragments were obtained from 80 embryos per sample according to an adapted protocol from Ignolia et al 2009. Embryos were incubated with 0.1 ug/ml cycloheximide in Methylene blue water for 5 min then snap frozen in 25ul Lysis buffer and clarified for 10 min at 10g 4degC. Supernatant was incubated with RNaseI and DNase at room temperature for 45 minutes with gentle mixing then digested extracts 50ul were overlain in a 100ul cushion of 1.8M sucrose in 20mM total Tris HCL ph8.0; 140mM KCl; 5 mM MgCl2; 100 ug/ml Cycloheximide; 0.5 mM DTT; 40U/ml SUPERas In Ambion #AM2694 for 14 h at 55.000 rpm in a TLS55 rotor in a Beckman TL100 ultracentrifuge. The bottom 30 ul was mixed with 4ul of PNK buffer and 4 ul of Proteinase K and incubated at 37degC for 30 minutes. RNA was extracted using Trizol then run on a 15% Urea gel to excise the 28 38 nt region. To construct barcoded Illumina small RNA libraries samples were eluted overnight in 300 mM NaOAc pH 5.5; 1 mM EDTA; 0.1U/ul SUPERas In Ambion #AM2694 followed by Ethanol precipitation. RFP and RNA input fragments were 3? dephosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer without xxx for 1 h at 37degC followed by 10 min incubation at 75degC and ethanol precipitation. Samples were resuspended and ligated to Illumina v1.5 three prime adapter using T4 RNA Ligase 2 truncated K227Q and RNAseOUT Recombinant Ribonuclease Inhibitor for 6h at 20degC then separated on a 10% Urea gel to extract the three prime ligation products. These were five prime phosphorylated with polynucleotide kinase in T4 polynucleotide kinase buffer with 1mM ATP for 30 min at 37degC and precipitated in ethanol. five prime ligation was performed using T4 RNA Ligase 1 for 6 hrs at 20degC with individual 100uM barcoded five prime adapters then separated on a 10% Urea gel. Gel purified samples were reverse transcribed using SuperScript II Reverse Transcriptase according to the Invitrogen protocol then amplified using Phusion High Fidelity DNA Polymerase. PC…   sample type:ribosome protected fragments|tissue:whole embryo|genotype:MZdicer mutant|developmental stage:2hpf GSM854432 GSM854432: Ribosome protected fragments MZdicer 2hpf; Danio rerio; RNA Seq GSM854432 1 GSM854432: Ribosome protected fragments MZdicer 2hpf 1   GEO Accession:GSM854432 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</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> SRP010040     Ribo_Dicer_2_A1.fq fastq 216257400.0 3003575.0 GSM854432 r1 0:72 A:66784432;C:51526758;G:47615177;T:50321714;N:9319 72       66784432 51526758 47615177 50321714 9319 SRX113350 SRS284294 SRA048903 GEO Giraldez Lab, Genetics, Yale University 1 6e-05   1e-05   0.99995   1.0   72   T   under 1.2% mapping rate illumina early_illumina unknown poly_a unknown bulk unknown unknown   United States 2011-12-27 Cleavage Embryo Whole Organism All anatomical structures

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