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4,921 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Whole Organism"

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experiment.library_selection >10

devstage_curation >10

technology 8

experiment.platform 6

devstage_curation_coarse 6

experiment.library_strategy 5

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 4,921 ✖

experiment.library_source 1

  • TRANSCRIPTOMIC · 4,921 ✖

experiment.library_layout 1

  • SINGLE · 4,921 ✖
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
60 60 DRR032764 DRX029570 DRS049969 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 shield 2 SAMD00028161   sample name:Dr shield 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:shield|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028161 DRX029570 Dr shield 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 SAMD00028161       3644397900.0 36443979.0 DRR032764 0:100 1:0 A:986071173;C:842367218;G:837686080;T:978236607;N:36822 100 0     986071173 842367218 837686080 978236607 36822 DRX029570 DRS049969 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 0.92419   0.08269   0.75558   0.47863   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
61 61 DRR032763 DRX029569 DRS049968 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 shield 1 SAMD00028160   sample name:Dr shield 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:shield|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028160 DRX029569 Dr shield 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 SAMD00028160       3834622000.0 38346220.0 DRR032763 0:100 1:0 A:1043352851;C:880011834;G:876775415;T:1034444253;N:37647 100 0     1043352851 880011834 876775415 1034444253 37647 DRX029569 DRS049968 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 0.92305   0.09126   0.75481   0.47587   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
62 62 DRR032762 DRX029568 DRS049967 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 50 individuals Dr prime5 6 3 SAMD00028159   sample name:Dr prime5 6 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028159 DRX029568 Dr prime5 6 3 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 SAMD00028159       3903332800.0 39033328.0 DRR032762 0:100 1:0 A:1050045822;C:908538410;G:900588661;T:1044116537;N:43370 100 0     1050045822 908538410 900588661 1044116537 43370 DRX029568 DRS049967 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 0.92761   0.07976   0.69126   0.46568   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
63 63 DRR032761 DRX029567 DRS049966 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 50 individuals Dr prime5 6 2 SAMD00028158   sample name:Dr prime5 6 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028158 DRX029567 Dr prime5 6 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 SAMD00028158       3678549700.0 36785497.0 DRR032761 0:100 1:0 A:986526644;C:857762765;G:853417738;T:980801764;N:40789 100 0     986526644 857762765 853417738 980801764 40789 DRX029567 DRS049966 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 0.92689   0.07872   0.6928   0.46577   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
64 64 DRR032760 DRX029566 DRS049965 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 50 individuals Dr prime5 6 1 SAMD00028157   sample name:Dr prime5 6 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime5 6|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028157 DRX029566 Dr prime5 6 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 SAMD00028157       3863129500.0 38631295.0 DRR032760 0:100 1:0 A:1035240477;C:901625010;G:895370149;T:1030851937;N:41927 100 0     1035240477 901625010 895370149 1030851937 41927 DRX029566 DRS049965 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 0.92337   0.07522   0.69315   0.46516   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
65 65 DRR032759 DRX029565 DRS049964 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 50 individuals Dr prime25 2 SAMD00028156   sample name:Dr prime25 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028156 DRX029565 Dr prime25 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 SAMD00028156       3750136100.0 37501361.0 DRR032759 0:100 1:0 A:1013528040;C:866734984;G:862431819;T:1007403208;N:38049 100 0     1013528040 866734984 862431819 1007403208 38049 DRX029565 DRS049964 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 0.92019   0.09079   0.68304   0.47083   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
66 66 DRR032758 DRX029564 DRS049963 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 50 individuals Dr prime25 1 SAMD00028155   sample name:Dr prime25 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:prime25|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028155 DRX029564 Dr prime25 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 SAMD00028155       3544862700.0 35448627.0 DRR032758 0:100 1:0 A:952135895;C:825841753;G:821757889;T:945087927;N:39236 100 0     952135895 825841753 821757889 945087927 39236 DRX029564 DRS049963 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 0.92229   0.08344   0.68525   0.466   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
67 67 DRR032757 DRX029563 DRS049962 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 97 individuals Dr bud 2 SAMD00028154   sample name:Dr bud 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028154 DRX029563 Dr bud 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 SAMD00028154       4104778200.0 41047782.0 DRR032757 0:100 1:0 A:1116316188;C:944738800;G:936257056;T:1107423486;N:42670 100 0     1116316188 944738800 936257056 1107423486 42670 DRX029563 DRS049962 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 0.92945   0.10493   0.73407   0.47824   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
68 68 DRR032756 DRX029562 DRS049961 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 bud 1 SAMD00028153   sample name:Dr bud 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:bud|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028153 DRX029562 Dr bud 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 SAMD00028153       4540291000.0 45402910.0 DRR032756 0:100 1:0 A:1237914068;C:1042346110;G:1033172731;T:1226799791;N:58300 100 0     1237914068 1042346110 1033172731 1226799791 58300 DRX029562 DRS049961 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 0.92628   0.10478   0.7391   0.46461   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Undetermined Embryo Whole Organism All anatomical structures
69 69 DRR032755 DRX029561 DRS049960 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 90epiboly 2 SAMD00028152   sample name:Dr 90epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028152 DRX029561 Dr 90epiboly 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 SAMD00028152       3572358600.0 35723586.0 DRR032755 0:100 1:0 A:971653450;C:821326559;G:816855636;T:962477457;N:45498 100 0     971653450 821326559 816855636 962477457 45498 DRX029561 DRS049960 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 0.92485   0.10642   0.74213   0.47012   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
70 70 DRR032754 DRX029560 DRS049959 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 90epiboly 1 SAMD00028151   sample name:Dr 90epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:90epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028151 DRX029560 Dr 90epiboly 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 SAMD00028151       3423980500.0 34239805.0 DRR032754 0:100 1:0 A:933088185;C:785251613;G:780911148;T:924686406;N:43148 100 0     933088185 785251613 780911148 924686406 43148 DRX029560 DRS049959 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 0.92436   0.10881   0.74255   0.47068   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
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
73 73 DRR032751 DRX029557 DRS049956 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 75epiboly 2 SAMD00028148   sample name:Dr 75epiboly 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028148 DRX029557 Dr 75epiboly 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 SAMD00028148       3252021500.0 32520215.0 DRR032751 0:100 1:0 A:885527595;C:746750899;G:742907892;T:876794123;N:40991 100 0     885527595 746750899 742907892 876794123 40991 DRX029557 DRS049956 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 0.92594   0.10181   0.74862   0.47789   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
74 74 DRR032750 DRX029556 DRS049955 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 75epiboly 1 SAMD00028147   sample name:Dr 75epiboly 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:75epiboly|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028147 DRX029556 Dr 75epiboly 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 SAMD00028147       3785053700.0 37850537.0 DRR032750 0:100 1:0 A:1029014798;C:870946157;G:867537069;T:1017508684;N:46992 100 0     1029014798 870946157 867537069 1017508684 46992 DRX029556 DRS049955 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 0.92346   0.10046   0.74921   0.47295   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Gastrula Embryo Whole Organism All anatomical structures
75 75 DRR032749 DRX029555 DRS049954 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 50 individuals Dr 72h 2 SAMD00028146   sample name:Dr 72h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028146 DRX029555 Dr 72h 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 SAMD00028146       3429795800.0 34297958.0 DRR032749 0:100 1:0 A:928062015;C:792470305;G:786930881;T:922296289;N:36310 100 0     928062015 792470305 786930881 922296289 36310 DRX029555 DRS049954 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 0.91821   0.09774   0.65437   0.46443   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Larval Larval Whole Organism All anatomical structures
76 76 DRR032748 DRX029554 DRS049953 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 50 individuals Dr 72h 1 SAMD00028145   sample name:Dr 72h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:72h Protruding mouth|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028145 DRX029554 Dr 72h 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 SAMD00028145       3897194500.0 38971945.0 DRR032748 0:100 1:0 A:1050989414;C:903225496;G:895783177;T:1047153493;N:42920 100 0     1050989414 903225496 895783177 1047153493 42920 DRX029554 DRS049953 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 0.92211   0.09393   0.65486   0.45971   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Larval Larval Whole Organism All anatomical structures
77 77 DRR032747 DRX029553 DRS049952 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 50 individuals Dr 6somite 2 SAMD00028144   sample name:Dr 6somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028144 DRX029553 Dr 6somite 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 SAMD00028144       3704431000.0 37044310.0 DRR032747 0:100 1:0 A:1001844161;C:856702913;G:850695568;T:995148798;N:39560 100 0     1001844161 856702913 850695568 995148798 39560 DRX029553 DRS049952 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 0.92633   0.09211   0.72107   0.47195   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Segmentation Embryo Whole Organism All anatomical structures
78 78 DRR032746 DRX029552 DRS049951 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 50 individuals Dr 6somite 1 SAMD00028143   sample name:Dr 6somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:6somite|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028143 DRX029552 Dr 6somite 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 SAMD00028143       3529311900.0 35293119.0 DRR032746 0:100 1:0 A:953957996;C:816824469;G:811403696;T:947089530;N:36209 100 0     953957996 816824469 811403696 947089530 36209 DRX029552 DRS049951 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 0.92437   0.09257   0.72113   0.47004   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Segmentation Embryo Whole Organism All anatomical structures
79 79 DRR032745 DRX029551 DRS049950 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 50 individuals Dr 60h 2 SAMD00028142   sample name:Dr 60h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028142 DRX029551 Dr 60h 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 SAMD00028142       3875337000.0 38753370.0 DRR032745 0:100 1:0 A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983 100 0     1042558903 899892111 896867583 1035981420 36983 DRX029551 DRS049950 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 0.91891   0.09445   0.66156   0.45564   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
80 80 DRR032744 DRX029550 DRS049949 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 50 individuals Dr 60h 1 SAMD00028141   sample name:Dr 60h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:60h Pec fin|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028141 DRX029550 Dr 60h 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 SAMD00028141       3538468200.0 35384682.0 DRR032744 0:100 1:0 A:960664313;C:812459988;G:809014008;T:956295205;N:34686 100 0     960664313 812459988 809014008 956295205 34686 DRX029550 DRS049949 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 0.91388   0.10346   0.66076   0.45203   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
81 81 DRR032743 DRX029549 DRS049948 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 50 individuals Dr 5day 3 SAMD00028140   sample name:Dr 5day 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028140 DRX029549 Dr 5day 3 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 SAMD00028140       3884716000.0 38847160.0 DRR032743 0:100 1:0 A:1040550584;C:905663425;G:904247323;T:1034215019;N:39649 100 0     1040550584 905663425 904247323 1034215019 39649 DRX029549 DRS049948 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 0.92219   0.08287   0.65863   0.47377   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Larval Larval Whole Organism All anatomical structures
82 82 DRR032742 DRX029548 DRS049947 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 50 individuals Dr 5day 2 SAMD00028139   sample name:Dr 5day 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028139 DRX029548 Dr 5day 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 SAMD00028139       3893708700.0 38937087.0 DRR032742 0:100 1:0 A:1050850168;C:899863467;G:897224776;T:1045729184;N:41105 100 0     1050850168 899863467 897224776 1045729184 41105 DRX029548 DRS049947 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 0.91671   0.0991   0.65161   0.47454   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Larval Larval Whole Organism All anatomical structures
83 83 DRR032741 DRX029547 DRS049946 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 50 individuals Dr 5day 1 SAMD00028138   sample name:Dr 5day 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:5day|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028138 DRX029547 Dr 5day 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 SAMD00028138       3807570600.0 38075706.0 DRR032741 0:100 1:0 A:1022590228;C:884655401;G:882546091;T:1017737883;N:40997 100 0     1022590228 884655401 882546091 1017737883 40997 DRX029547 DRS049946 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 0.9182   0.09442   0.65525   0.46661   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Larval Larval Whole Organism All anatomical structures
84 84 DRR032740 DRX029546 DRS049945 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 50 individuals Dr 48h 2 SAMD00028137   sample name:Dr 48h 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028137 DRX029546 Dr 48h 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 SAMD00028137       3702804700.0 37028047.0 DRR032740 0:100 1:0 A:993931475;C:862403562;G:857808891;T:988623734;N:37038 100 0     993931475 862403562 857808891 988623734 37038 DRX029546 DRS049945 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 0.92508   0.08526   0.68349   0.45769   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching Embryo Whole Organism All anatomical structures
85 85 DRR032739 DRX029545 DRS049944 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 50 individuals Dr 48h 1 SAMD00028136   sample name:Dr 48h 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:48h Long pec|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028136 DRX029545 Dr 48h 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 SAMD00028136       3980240400.0 39802404.0 DRR032739 0:100 1:0 A:1070497788;C:925240883;G:920038728;T:1064422474;N:40527 100 0     1070497788 925240883 920038728 1064422474 40527 DRX029545 DRS049944 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 0.92349   0.08681   0.67874   0.46565   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Hatching 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
88 88 DRR032736 DRX029542 DRS049941 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 zfs:0000015 2 SAMD00028133   sample name:Dr zfs:0000015 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:zfs:0000015|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028133 DRX029542 Dr zfs:0000015 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 SAMD00028133       3129028500.0 31290285.0 DRR032736 0:100 1:0 A:849515903;C:721550282;G:717777586;T:840154982;N:29747 100 0     849515903 721550282 717777586 840154982 29747 DRX029542 DRS049941 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 0.92724   0.07971   0.74657   0.47796   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Blastula Embryo Whole Organism All anatomical structures
89 89 DRR032735 DRX029541 DRS049940 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 zfs:0000015 1 SAMD00028132   sample name:Dr zfs:0000015 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:zfs:0000015|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028132 DRX029541 Dr zfs:0000015 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 SAMD00028132       4310219700.0 43102197.0 DRR032735 0:100 1:0 A:1169701983;C:993241399;G:986263558;T:1160969083;N:43677 100 0     1169701983 993241399 986263558 1160969083 43677 DRX029541 DRS049940 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 0.92609   0.07773   0.74349   0.47849   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Blastula 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
92 92 DRR032732 DRX029538 DRS049937 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 80 individuals Dr 14somite 3 SAMD00028129   sample name:Dr 14somite 3|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028129 DRX029538 Dr 14somite 3 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 SAMD00028129       3734610500.0 37346105.0 DRR032732 0:100 1:0 A:1009418541;C:863710067;G:858061383;T:1003378800;N:41709 100 0     1009418541 863710067 858061383 1003378800 41709 DRX029538 DRS049937 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 0.92401   0.08815   0.70816   0.46602   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Segmentation Embryo Whole Organism All anatomical structures
93 93 DRR032731 DRX029537 DRS049936 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 80 individuals Dr 14somite 2 SAMD00028128   sample name:Dr 14somite 2|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028128 DRX029537 Dr 14somite 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 SAMD00028128       3715174200.0 37151742.0 DRR032731 0:100 1:0 A:1000703508;C:862290629;G:858173468;T:993968396;N:38199 100 0     1000703508 862290629 858173468 993968396 38199 DRX029537 DRS049936 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 0.92491   0.0819   0.71068   0.46957   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Segmentation Embryo Whole Organism All anatomical structures
94 94 DRR032730 DRX029536 DRS049935 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 80 individuals Dr 14somite 1 SAMD00028127   sample name:Dr 14somite 1|strain:Riken WT Wild Type|tissue type:whole embryo|dev stage:14somite|genotype:wild type|phenotype:wild type|sex:male female and mixed                 Illumina HiSeq 2000 sequencing of SAMD00028127 DRX029536 Dr 14somite 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 SAMD00028127       3744386000.0 37443860.0 DRR032730 0:100 1:0 A:1014537326;C:864070910;G:859190201;T:1006549502;N:38061 100 0     1014537326 864070910 859190201 1006549502 38061 DRX029536 DRS049935 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 0.92378   0.08957   0.7068   0.47493   100   B   usable mapping rate illumina hiseq_era unknown other trueseq bulk unknown unknown   Japan 2017-09-20 Segmentation Embryo Whole Organism All anatomical structures
3016 3016 ERR1396840 ERX1468099 ERS1051447 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B12 SAMEA3864313 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#23 15616943 Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTGAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#23.cram cram 911394150.0 18227883.0 SC RUN 18732 2#23 0:50 A:264591252;C:227216187;G:236072241;T:183438530;N:75940 50       264591252 227216187 236072241 183438530 75940 ERX1468099 ERS1051447 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.58273   0.09754   0.87448   0.55833   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3017 3017 ERR1396839 ERX1468098 ERS1051446 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B10 SAMEA3864312 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864312|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#22 15616931 Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GAGTGG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#22.cram cram 242466400.0 4849328.0 SC RUN 18732 2#22 0:50 A:69326734;C:60104801;G:65507097;T:47507301;N:20467 50       69326734 60104801 65507097 47507301 20467 ERX1468098 ERS1051446 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60819   0.09544   0.87864   0.58472   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3018 3018 ERR1396838 ERX1468097 ERS1051445 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B3 SAMEA3864311 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864311|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#21 15616919 Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGTACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#21.cram cram 630737800.0 12614756.0 SC RUN 18732 2#21 0:50 A:180007611;C:161281943;G:164376347;T:125019243;N:52656 50       180007611 161281943 164376347 125019243 52656 ERX1468097 ERS1051445 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62407   0.10189   0.87825   0.57526   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3019 3019 ERR1396837 ERX1468096 ERS1051444 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A4 SAMEA3864310 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864310|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:33Z|INSDC status:public|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#20 15616907 Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTTTCG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#20.cram cram 488336450.0 9766729.0 SC RUN 18732 2#20 0:50 A:137910201;C:123586221;G:128373512;T:98425645;N:40871 50       137910201 123586221 128373512 98425645 40871 ERX1468096 ERS1051444 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.5453   0.11361   0.86594   0.58106   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3020 3020 ERR1396836 ERX1468095 ERS1051443 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A3 SAMEA3864309 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864309|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#19 15616895 Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGGCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#19.cram cram 502748050.0 10054961.0 SC RUN 18732 2#19 0:50 A:140684190;C:129525504;G:133998850;T:98497819;N:41687 50       140684190 129525504 133998850 98497819 41687 ERX1468095 ERS1051443 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.55085   0.11739   0.87077   0.6012   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3021 3021 ERR1396835 ERX1468094 ERS1051442 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A2 SAMEA3864308 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864308|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#18 15616883 Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTGAAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#18.cram cram 512343000.0 10246860.0 SC RUN 18732 2#18 0:50 A:149660992;C:130013834;G:134888430;T:97736324;N:43420 50       149660992 130013834 134888430 97736324 43420 ERX1468094 ERS1051442 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54809   0.11505   0.88254   0.5985   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3022 3022 ERR1396834 ERX1468093 ERS1051441 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A1 SAMEA3864307 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864307|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#17 15616871 Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GTCCGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#17.cram cram 296362850.0 5927257.0 SC RUN 18732 2#17 0:50 A:84251830;C:79653531;G:76748992;T:55683722;N:24775 50       84251830 79653531 76748992 55683722 24775 ERX1468093 ERS1051441 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.50115   0.10395   0.90185   0.6019   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3023 3023 ERR1396833 ERX1468092 ERS1051440 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C3 SAMEA3864306 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864306|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#16 15616954 Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CCGTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#16.cram cram 247427250.0 4948545.0 SC RUN 18732 2#16 0:50 A:69477894;C:64165990;G:64753499;T:49009156;N:20711 50       69477894 64165990 64753499 49009156 20711 ERX1468092 ERS1051440 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.66601   0.10439   0.88156   0.5519   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3024 3024 ERR1396832 ERX1468091 ERS1051439 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B4 SAMEA3864305 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864305|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:30Z|INSDC status:public|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#15 15616942 Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATGTCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#15.cram cram 268495550.0 5369911.0 SC RUN 18732 2#15 0:50 A:78316008;C:67311837;G:69086954;T:53758238;N:22513 50       78316008 67311837 69086954 53758238 22513 ERX1468091 ERS1051439 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61927   0.0935   0.89745   0.55698   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3025 3025 ERR1396831 ERX1468090 ERS1051438 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A7 SAMEA3864304 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864304|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#14 15616930 Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#14.cram cram 457637200.0 9152744.0 SC RUN 18732 2#14 0:50 A:131304805;C:115755054;G:118778813;T:91760838;N:37690 50       131304805 115755054 118778813 91760838 37690 ERX1468090 ERS1051438 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64717   0.09607   0.89832   0.56732   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3026 3026 ERR1396830 ERX1468089 ERS1051437 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A1 SAMEA3864303 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864303|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#13 15616918 Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence AGTCAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#13.cram cram 156613950.0 3132279.0 SC RUN 18732 2#13 0:50 A:45659102;C:39445557;G:40495414;T:31000827;N:13050 50       45659102 39445557 40495414 31000827 13050 ERX1468089 ERS1051437 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.65923   0.09289   0.90096   0.52171   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3027 3027 ERR1396829 ERX1468088 ERS1051436 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C1 SAMEA3864302 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864302|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#12 15616906 Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CTTGTA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#12.cram cram 370496150.0 7409923.0 SC RUN 18732 2#12 0:50 A:104657486;C:92274677;G:97465315;T:76068240;N:30432 50       104657486 92274677 97465315 76068240 30432 ERX1468088 ERS1051436 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64244   0.11811   0.86578   0.55798   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3028 3028 ERR1396828 ERX1468087 ERS1051435 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B3 SAMEA3864301 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864301|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#11 15616894 Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GGCTAC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#11.cram cram 136326100.0 2726522.0 SC RUN 18732 2#11 0:50 A:38914874;C:34737645;G:36229387;T:26432631;N:11563 50       38914874 34737645 36229387 26432631 11563 ERX1468087 ERS1051435 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60295   0.10315   0.89092   0.58169   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3029 3029 ERR1396827 ERX1468086 ERS1051434 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A12 SAMEA3864300 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864300|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:27Z|INSDC status:public|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#10 15616882 Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TAGCTT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#10.cram cram 257740250.0 5154805.0 SC RUN 18732 2#10 0:50 A:73736881;C:64681440;G:67096497;T:52203988;N:21444 50       73736881 64681440 67096497 52203988 21444 ERX1468086 ERS1051434 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62041   0.10196   0.89706   0.55474   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3030 3030 ERR1396826 ERX1468085 ERS1051433 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A10 SAMEA3864299 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#9 15616870 Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GATCAG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#9.cram cram 7356000.0 147120.0 SC RUN 18732 2#9 0:50 A:2152284;C:1844982;G:1920243;T:1437897;N:594 50       2152284 1844982 1920243 1437897 594 ERX1468085 ERS1051433 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60239   0.10502   0.91084   0.55869   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3031 3031 ERR1396825 ERX1468084 ERS1051432 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha C1 SAMEA3864298 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#8 15616953 Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACTTGA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#8.cram cram 454519900.0 9090398.0 SC RUN 18732 2#8 0:50 A:133717355;C:117574792;G:114940340;T:88249706;N:37707 50       133717355 117574792 114940340 88249706 37707 ERX1468084 ERS1051432 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51063   0.10053   0.88572   0.60434   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3032 3032 ERR1396824 ERX1468083 ERS1051431 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A9 SAMEA3864297 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#7 15616941 Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CAGATC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#7.cram cram 288165650.0 5763313.0 SC RUN 18732 2#7 0:50 A:83874531;C:74578491;G:74739497;T:54949008;N:24123 50       83874531 74578491 74739497 54949008 24123 ERX1468083 ERS1051431 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.56561   0.10234   0.88278   0.59066   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3033 3033 ERR1396823 ERX1468082 ERS1051430 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A6 SAMEA3864296 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#6 15616929 Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence GCCAAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#6.cram cram 234507600.0 4690152.0 SC RUN 18732 2#6 0:50 A:67284766;C:59565829;G:61407599;T:46229970;N:19436 50       67284766 59565829 61407599 46229970 19436 ERX1468082 ERS1051430 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64334   0.10252   0.88905   0.5695   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3034 3034 ERR1396822 ERX1468081 ERS1051429 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A1 SAMEA3864295 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:24Z|INSDC status:public|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#5 15616917 Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ACAGTG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#5.cram cram 161797350.0 3235947.0 SC RUN 18732 2#5 0:50 A:46711991;C:40739475;G:42456048;T:31876390;N:13446 50       46711991 40739475 42456048 31876390 13446 ERX1468081 ERS1051429 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64666   0.09851   0.90508   0.56607   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3035 3035 ERR1396821 ERX1468080 ERS1051428 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B12 SAMEA3864294 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:23Z|INSDC status:public|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#4 15616905 Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TGACCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#4.cram cram 393377600.0 7867552.0 SC RUN 18732 2#4 0:50 A:115292812;C:103803007;G:98535312;T:75713409;N:33060 50       115292812 103803007 98535312 75713409 33060 ERX1468080 ERS1051428 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51888   0.1037   0.89948   0.59445   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3036 3036 ERR1396820 ERX1468079 ERS1051427 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B10 SAMEA3864293 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#3 15616893 Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence TTAGGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#3.cram cram 211138300.0 4222766.0 SC RUN 18732 2#3 0:50 A:60487130;C:53019786;G:55472125;T:42141858;N:17401 50       60487130 53019786 55472125 42141858 17401 ERX1468079 ERS1051427 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57434   0.11571   0.88633   0.6058   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3037 3037 ERR1396819 ERX1468078 ERS1051426 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B7 SAMEA3864292 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#2 15616881 Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence CGATGT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#2.cram cram 318903600.0 6378072.0 SC RUN 18732 2#2 0:50 A:91235181;C:80984947;G:84861359;T:61795663;N:26450 50       91235181 80984947 84861359 61795663 26450 ERX1468078 ERS1051426 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57408   0.11398   0.87629   0.60954   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3038 3038 ERR1396818 ERX1468077 ERS1051425 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B1 SAMEA3864291 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 2#1 15616869 Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 2. This submission includes reads tagged with the sequence ATCACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_2#1.cram cram 411180300.0 8223606.0 SC RUN 18732 2#1 0:50 A:118946374;C:103897659;G:107565667;T:80736319;N:34281 50       118946374 103897659 107565667 80736319 34281 ERX1468077 ERS1051425 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60674   0.11483   0.90258   0.54833   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3040 3040 ERR1396816 ERX1468075 ERS1051447 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B12 SAMEA3864313 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864313|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:35Z|INSDC status:public|Submitter Id:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a7dbab0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#23 15616943 Illumina sequencing of library 15616943 constructed from sample accession ERS1051447 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTGAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#23.cram cram 932669450.0 18653389.0 SC RUN 18732 1#23 0:50 A:270743929;C:232449590;G:241669732;T:187716399;N:89800 50       270743929 232449590 241669732 187716399 89800 ERX1468075 ERS1051447 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.58314   0.09813   0.87373   0.55534   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3041 3041 ERR1396815 ERX1468074 ERS1051446 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B10 SAMEA3864312 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864312|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a70e970 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#22 15616931 Illumina sequencing of library 15616931 constructed from sample accession ERS1051446 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GAGTGG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#22.cram cram 247740600.0 4954812.0 SC RUN 18732 1#22 0:50 A:70832472;C:61402287;G:66930146;T:48552217;N:23478 50       70832472 61402287 66930146 48552217 23478 ERX1468074 ERS1051446 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60866   0.09645   0.87842   0.56581   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3042 3042 ERR1396814 ERX1468073 ERS1051445 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 B3 SAMEA3864311 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864311|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:34Z|INSDC status:public|Submitter Id:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a6aa7e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#21 15616919 Illumina sequencing of library 15616919 constructed from sample accession ERS1051445 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGTACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#21.cram cram 644730800.0 12894616.0 SC RUN 18732 1#21 0:50 A:183986486;C:164794735;G:168072875;T:127815308;N:61396 50       183986486 164794735 168072875 127815308 61396 ERX1468073 ERS1051445 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.62529   0.10255   0.87673   0.58496   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3043 3043 ERR1396813 ERX1468072 ERS1051444 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A4 SAMEA3864310 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864310|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:33Z|INSDC status:public|Submitter Id:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a61a730 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#20 15616907 Illumina sequencing of library 15616907 constructed from sample accession ERS1051444 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTTTCG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#20.cram cram 498997400.0 9979948.0 SC RUN 18732 1#20 0:50 A:140918075;C:126256924;G:131206962;T:100567098;N:48341 50       140918075 126256924 131206962 100567098 48341 ERX1468072 ERS1051444 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54672   0.11372   0.8659   0.58386   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3044 3044 ERR1396812 ERX1468071 ERS1051443 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A3 SAMEA3864309 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864309|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a5a0610 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#19 15616895 Illumina sequencing of library 15616895 constructed from sample accession ERS1051443 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGGCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#19.cram cram 513060400.0 10261208.0 SC RUN 18732 1#19 0:50 A:143572990;C:132143361;G:136785883;T:100508957;N:49209 50       143572990 132143361 136785883 100508957 49209 ERX1468071 ERS1051443 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.55168   0.11683   0.86868   0.59303   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3045 3045 ERR1396811 ERX1468070 ERS1051442 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A2 SAMEA3864308 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864308|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:32Z|INSDC status:public|Submitter Id:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a537660 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#18 15616883 Illumina sequencing of library 15616883 constructed from sample accession ERS1051442 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTGAAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#18.cram cram 522864750.0 10457295.0 SC RUN 18732 1#18 0:50 A:152695334;C:132665110;G:137681171;T:99772629;N:50506 50       152695334 132665110 137681171 99772629 50506 ERX1468070 ERS1051442 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.54885   0.11528   0.88176   0.60373   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3046 3046 ERR1396810 ERX1468069 ERS1051441 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph230 dgcr8 A1 SAMEA3864307 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864307|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dgcr8 allele sa223. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a4c4a70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#17 15616871 Illumina sequencing of library 15616871 constructed from sample accession ERS1051441 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GTCCGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#17.cram cram 302165250.0 6043305.0 SC RUN 18732 1#17 0:50 A:85905345;C:81184773;G:78275206;T:56770744;N:29182 50       85905345 81184773 78275206 56770744 29182 ERX1468069 ERS1051441 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.50199   0.10346   0.90118   0.59572   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3047 3047 ERR1396809 ERX1468068 ERS1051440 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C3 SAMEA3864306 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864306|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:31Z|INSDC status:public|Submitter Id:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a3ba8a0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#16 15616954 Illumina sequencing of library 15616954 constructed from sample accession ERS1051440 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CCGTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#16.cram cram 252866050.0 5057321.0 SC RUN 18732 1#16 0:50 A:71001103;C:65550329;G:66199420;T:50091388;N:23810 50       71001103 65550329 66199420 50091388 23810 ERX1468068 ERS1051440 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.66563   0.10454   0.88239   0.53964   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3048 3048 ERR1396808 ERX1468067 ERS1051439 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B4 SAMEA3864305 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864305|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:30Z|INSDC status:public|Submitter Id:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a319680 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#15 15616942 Illumina sequencing of library 15616942 constructed from sample accession ERS1051439 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATGTCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#15.cram cram 274471250.0 5489425.0 SC RUN 18732 1#15 0:50 A:80060226;C:68799356;G:70635515;T:54950129;N:26024 50       80060226 68799356 70635515 54950129 26024 ERX1468067 ERS1051439 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61964   0.09406   0.89402   0.55473   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3049 3049 ERR1396807 ERX1468066 ERS1051438 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A7 SAMEA3864304 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864304|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a2a6a90 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#14 15616930 Illumina sequencing of library 15616930 constructed from sample accession ERS1051438 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTTCC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#14.cram cram 467847600.0 9356952.0 SC RUN 18732 1#14 0:50 A:134225837;C:118320475;G:121443773;T:93812243;N:45272 50       134225837 118320475 121443773 93812243 45272 ERX1468066 ERS1051438 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64705   0.096   0.8983   0.56022   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3050 3050 ERR1396806 ERX1468065 ERS1051437 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A1 SAMEA3864303 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864303|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:29Z|INSDC status:public|Submitter Id:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a238cc0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#13 15616918 Illumina sequencing of library 15616918 constructed from sample accession ERS1051437 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence AGTCAA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#13.cram cram 160243100.0 3204862.0 SC RUN 18732 1#13 0:50 A:46708835;C:40347424;G:41434539;T:31737029;N:15273 50       46708835 40347424 41434539 31737029 15273 ERX1468065 ERS1051437 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.65975   0.09405   0.90065   0.54178   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3051 3051 ERR1396805 ERX1468064 ERS1051436 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer C1 SAMEA3864302 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864302|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a1b9d80 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#12 15616906 Illumina sequencing of library 15616906 constructed from sample accession ERS1051436 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CTTGTA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#12.cram cram 378715650.0 7574313.0 SC RUN 18732 1#12 0:50 A:106991982;C:94292878;G:99663404;T:77730801;N:36585 50       106991982 94292878 99663404 77730801 36585 ERX1468064 ERS1051436 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64513   0.11804   0.86525   0.55346   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3052 3052 ERR1396804 ERX1468063 ERS1051435 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer B3 SAMEA3864301 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864301|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:28Z|INSDC status:public|Submitter Id:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a0d93c0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#11 15616894 Illumina sequencing of library 15616894 constructed from sample accession ERS1051435 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GGCTAC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#11.cram cram 139094000.0 2781880.0 SC RUN 18732 1#11 0:50 A:39702275;C:35436377;G:36969525;T:26972594;N:13229 50       39702275 35436377 36969525 26972594 13229 ERX1468063 ERS1051435 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60357   0.10386   0.88872   0.5774   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3053 3053 ERR1396803 ERX1468062 ERS1051434 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A12 SAMEA3864300 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864300|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:27Z|INSDC status:public|Submitter Id:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:2a075230 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#10 15616882 Illumina sequencing of library 15616882 constructed from sample accession ERS1051434 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TAGCTT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#10.cram cram 263295150.0 5265903.0 SC RUN 18732 1#10 0:50 A:75332297;C:66059671;G:68562462;T:53315439;N:25281 50       75332297 66059671 68562462 53315439 25281 ERX1468062 ERS1051434 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.61939   0.10112   0.89613   0.55542   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3054 3054 ERR1396802 ERX1468061 ERS1051433 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph229 dicer A10 SAMEA3864299 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864299|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for dicer allele sa9205. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29ffff30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#9 15616870 Illumina sequencing of library 15616870 constructed from sample accession ERS1051433 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GATCAG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#9.cram cram 7506900.0 150138.0 SC RUN 18732 1#9 0:50 A:2194276;C:1883363;G:1959471;T:1468994;N:796 50       2194276 1883363 1959471 1468994 796 ERX1468061 ERS1051433 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60026   0.10518   0.91106   0.55508   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3055 3055 ERR1396801 ERX1468060 ERS1051432 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha C1 SAMEA3864298 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864298|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:26Z|INSDC status:public|Submitter Id:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29f306e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#8 15616953 Illumina sequencing of library 15616953 constructed from sample accession ERS1051432 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACTTGA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#8.cram cram 464447300.0 9288946.0 SC RUN 18732 1#8 0:50 A:136629424;C:120103988;G:117495447;T:90173901;N:44540 50       136629424 120103988 117495447 90173901 44540 ERX1468060 ERS1051432 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51298   0.10188   0.88434   0.6034   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3056 3056 ERR1396800 ERX1468059 ERS1051431 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A9 SAMEA3864297 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864297|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e942e0 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#7 15616941 Illumina sequencing of library 15616941 constructed from sample accession ERS1051431 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CAGATC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#7.cram cram 294666500.0 5893330.0 SC RUN 18732 1#7 0:50 A:85765921;C:76239559;G:76452231;T:56180868;N:27921 50       85765921 76239559 76452231 56180868 27921 ERX1468059 ERS1051431 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.56455   0.10217   0.88286   0.60374   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3057 3057 ERR1396799 ERX1468058 ERS1051430 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A6 SAMEA3864296 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864296|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:25Z|INSDC status:public|Submitter Id:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29e06940 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#6 15616929 Illumina sequencing of library 15616929 constructed from sample accession ERS1051430 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence GCCAAT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#6.cram cram 239549350.0 4790987.0 SC RUN 18732 1#6 0:50 A:68726161;C:60828350;G:62739441;T:47232484;N:22914 50       68726161 60828350 62739441 47232484 22914 ERX1468058 ERS1051430 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64469   0.1021   0.88878   0.58044   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3058 3058 ERR1396798 ERX1468057 ERS1051429 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha A1 SAMEA3864295 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864295|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:24Z|INSDC status:public|Submitter Id:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample wild type for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29d74180 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#5 15616917 Illumina sequencing of library 15616917 constructed from sample accession ERS1051429 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ACAGTG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#5.cram cram 165341300.0 3306826.0 SC RUN 18732 1#5 0:50 A:47735538;C:41622088;G:43392205;T:32575765;N:15704 50       47735538 41622088 43392205 32575765 15704 ERX1468057 ERS1051429 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.64704   0.09836   0.90534   0.56172   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3059 3059 ERR1396797 ERX1468056 ERS1051428 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B12 SAMEA3864294 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864294|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:23Z|INSDC status:public|Submitter Id:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29cf7950 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#4 15616905 Illumina sequencing of library 15616905 constructed from sample accession ERS1051428 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TGACCA. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#4.cram cram 401336200.0 8026724.0 SC RUN 18732 1#4 0:50 A:117609087;C:105872656;G:100576681;T:77238881;N:38895 50       117609087 105872656 100576681 77238881 38895 ERX1468056 ERS1051428 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.51741   0.10352   0.89749   0.58497   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3060 3060 ERR1396796 ERX1468055 ERS1051427 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B10 SAMEA3864293 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864293|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29c84d60 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#3 15616893 Illumina sequencing of library 15616893 constructed from sample accession ERS1051427 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence TTAGGC. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#3.cram cram 214767600.0 4295352.0 SC RUN 18732 1#3 0:50 A:61527319;C:53911904;G:56445139;T:42862938;N:20300 50       61527319 53911904 56445139 42862938 20300 ERX1468055 ERS1051427 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57363   0.11614   0.88487   0.61011   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3061 3061 ERR1396795 ERX1468054 ERS1051426 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B7 SAMEA3864292 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864292|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:56Z|INSDC last update:2016 02 03T09:48:22Z|INSDC status:public|Submitter Id:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29b1df30 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#2 15616881 Illumina sequencing of library 15616881 constructed from sample accession ERS1051426 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence CGATGT. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#2.cram cram 326025150.0 6520503.0 SC RUN 18732 1#2 0:50 A:93261648;C:82767834;G:86798075;T:63166259;N:31334 50       93261648 82767834 86798075 63166259 31334 ERX1468054 ERS1051426 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.57333   0.11365   0.87422   0.60838   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
3062 3062 ERR1396794 ERX1468053 ERS1051425 ERP013615 PRJEB12173 Transcriptome profiling of zebrafish small RNA from drosha dgcr8 or dicer knockouts Transcriptome_profiling_of_zebrafish_small_RNA_from_drosha__dgcr8_or_dicer_knockouts-sc-4011 Transcriptome Analysis Small RNA data was generated from zebrafish embryos at 5 dpf and genotyped for drosha dicer or dgcr8b to identify wild type heterozygous and homozygous knockout embryos. ArrayExpress:E ERAD 449     zmp ph228 drosha B1 SAMEA3864291 Wellcome Sanger Institute ArrayExpress DevelopmentalStage:ZFS:0000037|ArrayExpress OrganismPart:Whole embryo|ArrayExpress Species:Danio rerio|ENA first public:2016 05 03|ENA last update:2016 02 03|External Id:SAMEA3864291|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2016 05 03T14:21:55Z|INSDC last update:2016 02 03T09:48:20Z|INSDC status:public|Submitter Id:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|common name:zebrafish|sample description:Sample homozygous for drosha allele sa191. Total RNA from a 5 dpf zebrafish embryo treated with DNase.|sample name:29904d70 99a3 11e5 bdcf 3c4a9275d6c6|strain:mixed                 Illumina HiSeq 2500 sequencing SC EXP 18732 1#1 15616869 Illumina sequencing of library 15616869 constructed from sample accession ERS1051425 for study accession ERP013615. This is part of an Illumina multiplexed sequencing run 18732 1. This submission includes reads tagged with the sequence ATCACG. Small RNA miRNA   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP013615 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2016 05 03|ENA LAST UPDATE:2018 11 16 18732_1#1.cram cram 419669000.0 8393380.0 SC RUN 18732 1#1 0:50 A:121378853;C:106010609;G:109826454;T:82412717;N:40367 50       121378853 106010609 109826454 82412717 40367 ERX1468053 ERS1051425 ERA612385 European Nucleotide Archive Wellcome Sanger Institute 1 0.60815   0.11567   0.90289   0.5657   50   B   usable mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United Kingdom 2016-02-03 Larval Larval Whole Organism All anatomical structures
9764 9764 ERR3454281 ERX3476201 ERS360451 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224102 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224102|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 4. A 5 base indexing sequence CAAGA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 sibling sc 2013 10 17T10:16:28Z 1727409|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     659815100.0 13196302.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 6 0:50 A:163494131;C:142490716;G:153472608;T:200319869;N:37776 50       163494131 142490716 153472608 200319869 37776 ERX3476201 ERS360451 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00278   0.00206   0.99922   0.24031   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9765 9765 ERR3454280 ERX3476200 ERS360450 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224101 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224101|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype32 clutch 4. A 5 base indexing sequence CGCAA is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 4 mutant sc 2013 10 17T10:16:27Z 1727408|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     1031629900.0 20632598.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 5 0:50 A:266496533;C:234318648;G:214719546;T:316013013;N:82160 50       266496533 234318648 214719546 316013013 82160 ERX3476200 ERS360450 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.003   0.00187   0.99902   0.27272   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9766 9766 ERR3454279 ERX3476199 ERS360449 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224100 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224100|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence GCACG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 sibling sc 2013 10 17T10:16:26Z 1727407|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     547730200.0 10954604.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 4 0:50 A:142048050;C:118592881;G:112867934;T:174179317;N:42018 50       142048050 118592881 112867934 174179317 42018 ERX3476199 ERS360449 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00355   0.00226   0.99902   0.30487   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9767 9767 ERR3454278 ERX3476198 ERS360448 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224099 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:47:37Z|External Id:SAMEA2224099|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:47:37Z|INSDC status:public|Submitter Id:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 3. A 5 base indexing sequence CAGAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 3 mutant sc 2013 10 17T10:16:24Z 1727406|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     844323050.0 16886461.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 3 0:50 A:219263127;C:181661743;G:173433057;T:269898556;N:66567 50       219263127 181661743 173433057 269898556 66567 ERX3476198 ERS360448 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00523   0.00319   0.99892   0.2637   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9768 9768 ERR3454277 ERX3476197 ERS360447 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224098 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:50:06Z|External Id:SAMEA2224098|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:50:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically normal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence AGAAG is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 sibling sc 2013 10 17T10:16:23Z 1727405|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     600000000.0 12000000.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 2 0:50 A:153130383;C:136248892;G:127363796;T:183213089;N:43840 50       153130383 136248892 127363796 183213089 43840 ERX3476197 ERS360447 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00372   0.00211   0.99888   0.31649   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9769 9769 ERR3454276 ERX3476196 ERS360446 ERP116513 PRJEB33700 Regulation of Dot Icm effectors translocation by T4SS GGDEF EAL proteins in Legionella pneumophila ena-STUDY-CIRI-Inserm-U1111-26-07-2019-08:05:36:132-1961 Other Legionella pneumophila is a waterborne bacterium that can replicate in a variety of host cells from environmental amoebae to human macrophages. Its virulence traits are subject to complex regulation that involves some signaling pathways dependent on cyclic di GMP. Cyclic di GMP is a second messenger that can result in transcriptional translational or post translational control of targets including secretion systems. We are particularly interested in the c di GMP metabolizing enzyme Lpl0780/Lpp0809 needed for the early steps of intracellular cycle and the appropriate translocation of bacterial effectors by Dot/Icm T4SS. Comparative transcriptomic analysis was performed from the RNA seq data of the Lens Wild Type strain and the ?lpl0780 mutant using DESeq2 package on normalized gene read counts. The results showed that only 12 genes among 2966 were significantly differentially expressed P < 0.01 and log2 fold change of >1 or < 1 between ?lpl0780 strain and the WT Lens strain. However the fold changes remain quite weak and moreover none of these genes can be connected to T4SS or effectors. These results suggest that Lpl0780/Lpp0809 acts at a post transcriptional level on the translocation of effectors. ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26       SAMEA2224097 SC ArrayExpress DevelopmentalStage:Hatching long pec pec fin ZFS:0000033 ZFS:0000034|ArrayExpress OrganismPart:Whole Embryo|ArrayExpress Species:Danio rerio|ENA FIRST PUBLIC:2014 03 04T09:16:47Z|ENA LAST UPDATE:2018 03 08T16:49:06Z|External Id:SAMEA2224097|INSDC center name:SC|INSDC first public:2014 03 04T09:16:47Z|INSDC last update:2018 03 08T16:49:06Z|INSDC status:public|Submitter Id:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|common name:zebrafish|sample description:3 prime end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 32 clutch 2. A 5 base indexing sequence GAGGC is bases 6 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi bin/Projects/D rerio/zmp/search.pl?q=zmp ph32|sample name:ZMP phenotype 32 2 mutant sc 2013 10 17T10:16:20Z 1727404|scientific name:Danio rerio|strain:mixed                 Illumina HiSeq 2500 sequencing ena EXPERIMENT CIRI Inserm U1111 26 07 2019 18:33:36:193 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   ERP116513 Illumina HiSeq 2500 sequencing ENA FIRST PUBLIC:2019 09 25|ENA LAST UPDATE:2019 07 26     600000000.0 12000000.0 ena RUN CIRI Inserm U1111 26 07 2019 18:33:36:193 1 0:50 A:153852410;C:135392627;G:125428239;T:185280608;N:46116 50       153852410 135392627 125428239 185280608 46116 ERX3476196 ERS360446 ERA2051096 CIRI-Inserm-U1111|European Nucleotide Archive CIRI-Inserm-U1111 1 0.00545   0.00291   0.9988   0.31681   50   T   under 1.2% mapping rate illumina hiseq_era 3prime cdna_unspecified unknown bulk unknown unknown   France 2014-03-04 Hatching Embryo Whole Organism All anatomical structures
9803 9803 ERR3909553 ERX3918377 ERS4309135 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total3 SAMEA6544760 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544760|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total3 s Total3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal3_TCGACG_L003_R1_001.fastq.gz fastq 652379310.0 14497318.0 E MTAB 8795:Total3 0:45 1:0 A:150840591;C:135992123;G:240098326;T:125390188;N:58082 45 0     150840591 135992123 240098326 125390188 58082 ERX3918377 ERS4309135 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00539   0.00111   0.99582   0.74079   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9804 9804 ERR3909552 ERX3918376 ERS4309134 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total2 SAMEA6544759 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544759|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total2 s Total2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal2_TATAGC_L003_R1_001.fastq.gz fastq 457981740.0 10177372.0 E MTAB 8795:Total2 0:45 1:0 A:108846441;C:95327665;G:163111561;T:90654528;N:41545 45 0     108846441 95327665 163111561 90654528 41545 ERX3918376 ERS4309134 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00612   0.00144   0.99387   0.66666   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9805 9805 ERR3909551 ERX3918375 ERS4309133 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Total1 SAMEA6544758 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544758|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Total1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:unsorted whole organism|organism part:whole organism|sample name:E MTAB 8795:Total1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Total1 s Total1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:unsorted whole organism OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteTotal1_GTATAC_L003_R1_001.fastq.gz fastq 778934655.0 17309659.0 E MTAB 8795:Total1 0:45 1:0 A:175694794;C:165046556;G:285795545;T:152324198;N:73562 45 0     175694794 165046556 285795545 152324198 73562 ERX3918375 ERS4309133 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.0048   0.00098   0.99492   0.69892   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9806 9806 ERR3909550 ERX3918374 ERS4309132 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red3 SAMEA6544757 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544757|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red3 s Red3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed3_CACGAT_L003_R1_001.fastq.gz fastq 980271990.0 21783822.0 E MTAB 8795:Red3 0:45 1:0 A:231772782;C:201265416;G:341867307;T:205267905;N:98580 45 0     231772782 201265416 341867307 205267905 98580 ERX3918374 ERS4309132 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.0047   0.00138   0.99366   0.64343   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9807 9807 ERR3909549 ERX3918373 ERS4309131 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red2 SAMEA6544756 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544756|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red2 s Red2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed2_ATCGTG_L003_R1_001.fastq.gz fastq 755095185.0 16779893.0 E MTAB 8795:Red2 0:45 1:0 A:173488674;C:161696782;G:267896203;T:151943387;N:70139 45 0     173488674 161696782 267896203 151943387 70139 ERX3918373 ERS4309131 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00548   0.00113   0.99415   0.65826   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9808 9808 ERR3909548 ERX3918372 ERS4309130 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Red1 SAMEA6544755 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544755|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Red1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:G1 slow cycling|organism part:whole organism|sample name:E MTAB 8795:Red1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Red1 s Red1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:G1 slow cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteRed1_ACAGAT_L003_R1_001.fastq.gz fastq 755180370.0 16781786.0 E MTAB 8795:Red1 0:45 1:0 A:179369537;C:157573419;G:260889303;T:157277751;N:70360 45 0     179369537 157573419 260889303 157277751 70360 ERX3918372 ERS4309130 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00451   0.00099   0.99314   0.66248   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9809 9809 ERR3909547 ERX3918371 ERS4309129 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green3 SAMEA6544754 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544754|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green3|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green3|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green3 s Green3 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen3_GAGTGA_L003_R1_001.fastq.gz fastq 819288855.0 18206419.0 E MTAB 8795:Green3 0:45 1:0 A:189173618;C:170597494;G:286250625;T:173188944;N:78174 45 0     189173618 170597494 286250625 173188944 78174 ERX3918371 ERS4309129 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00439   0.001   0.99377   0.68367   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9810 9810 ERR3909546 ERX3918370 ERS4309128 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green2 SAMEA6544753 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544753|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green2|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green2|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green2 s Green2 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen2_CTGACG_L003_R1_001.fastq.gz fastq 697971375.0 15510475.0 E MTAB 8795:Green2 0:45 1:0 A:160028926;C:147075253;G:245773112;T:145025474;N:68610 45 0     160028926 147075253 245773112 145025474 68610 ERX3918370 ERS4309128 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00489   0.00085   0.99586   0.80163   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9811 9811 ERR3909545 ERX3918369 ERS4309127 ERP120006 PRJEB36776 CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E-MTAB-8795 Transcriptome Analysis The core promoter a stretch of DNA surrounding the transcription start site TSS is a major integration point for regulatory signals controlling gene transcription. Cellular differentiation is marked by divergence in transcriptional repertoire and cell cycling behaviour between cells of different fates. The role promoter associated gene regulatory networks play in development associated transitions in cell cycle dynamics is poorly understood. This study demonstrates in a vertebrate embryo how core promoter variations define transcriptional output in cells transitioning from a proliferative to cell lineage specifying phenotype. Assessment of cell proliferation across zebrafish embryo development using the FUCCI transgenic cell cycle phase marker revealed a spatial and lineage specific separation in cell cycling behaviour. To investigate the role differential promoter usage plays in this process cap analysis of gene expression CAGE was performed on cells segregated by cycling dynamics. ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 13   Protocols: Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Green1 SAMEA6544752 UNIVERSITY OF BIRMINGHAM ENA FIRST PUBLIC:2020 06 19T17:05:18Z|ENA LAST UPDATE:2020 02 13T15:36:56Z|External Id:SAMEA6544752|INSDC center name:UNIVERSITY OF BIRMINGHAM|INSDC first public:2020 06 19T17:05:18Z|INSDC last update:2020 02 13T15:36:56Z|INSDC status:public|Submitter Id:E MTAB 8795:Green1|age:14|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|fraction:S/G2/M rapid cycling|organism part:whole organism|sample name:E MTAB 8795:Green1|scientific name:Danio rerio|sex:not available|strain:Dual FUCCI                 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red E MTAB 8795:Green1 s Green1 s CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red Zebrafish were dechorionated and selected at the 14 somite stage 14 hpf The embryos were dissociated into a single cell suspension using enzyme free cell dissociation buffer PBS based Gibco. Dissociated cells were pelleted and resuspended in Hanks balanced salt solution without xxx chloride or magnesium sulphate Sigma for sorting. Cells were fluorescence associated cell sorted FACS into populations displaying red and green fluorescence. RNA was extracted from isolated cells using the miRNeasy kit Qiagen. RNA quality was analysed by capillary electrophoresis Bioanalyzer 2100 Agilent. All samples had an RNA integrity number RIN >9. NanoCAGE libraries were generated following a protocol described in: Poulain S. Kato S. Arnaud O. Morlighem J.E. Suzuki M. Plessy C. and Harbers M. 2017 NanoCAGE: A Method for the Analysis of Coding and Noncoding five prime Capped Transcriptomes. Methods Mol Biol 1543 57 109. Experimental Factor: fraction:S/G2/M rapid cycling OTHER TRANSCRIPTOMIC CAGE SINGLE ILLUMINA Illumina HiSeq 2500   ERP120006 Illumina HiSeq 2500 sequencing; CAGE seq of zebrafish cells extracted at the 14 somite stage and segregated by cell cycle dynamics e.g. fast green vs slow red ENA FIRST PUBLIC:2020 06 19|ENA LAST UPDATE:2020 02 25 14SomiteGreen1_CACTGA_L003_R1_001.fastq.gz fastq 826595640.0 18368792.0 E MTAB 8795:Green1 0:45 1:0 A:193728088;C:171605661;G:287824557;T:173352680;N:84654 45 0     193728088 171605661 287824557 173352680 84654 ERX3918369 ERS4309127 ERA2381432 UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive UNIVERSITY OF BIRMINGHAM|European Nucleotide Archive 1 0.00505   0.00101   0.99287   0.58198   45   T   under 1.2% mapping rate illumina hiseq_era unknown cage unknown bulk unknown unknown   United Kingdom 2020-02-13 Segmentation Embryo Whole Organism All anatomical structures
9825 9825 ERR2102841 ERX2160152 ERS1883528 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N3 nabu RNA SAMEA104224510 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224510|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N3 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N3 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N3 nabu RNA s N3 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N3_R1_all.fastq.gz fastq 1410139550.0 18670564.0 E MTAB 5992:N3 nabu RNA 0:75.53 1:0 A:353294009;C:340727934;G:322476371;T:393200193;N:441043 75 0     353294009 340727934 322476371 393200193 441043 ERX2160152 ERS1883528 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95434   0.08906   0.66935   0.47788   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9826 9826 ERR2102840 ERX2160151 ERS1883527 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N2 nabu RNA SAMEA104224509 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224509|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N2 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N2 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N2 nabu RNA s N2 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N2_R1_all.fastq.gz fastq 1478621168.0 19576865.0 E MTAB 5992:N2 nabu RNA 0:75.53 1:0 A:369453299;C:359092235;G:341176884;T:408389810;N:508940 75 0     369453299 359092235 341176884 408389810 508940 ERX2160151 ERS1883527 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95582   0.08202   0.67718   0.47812   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9827 9827 ERR2102839 ERX2160150 ERS1883526 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 N1 nabu RNA SAMEA104224508 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224508|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:N1 nabu RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:N1 nabu RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:N1 nabu RNA s N1 nabu RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:NaBu|Experimental Factor: dose:2 RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 N1_R1_all.fastq.gz fastq 1531713181.0 20277882.0 E MTAB 5992:N1 nabu RNA 0:75.54 1:0 A:386600603;C:373317031;G:350339456;T:420938891;N:517200 75 0     386600603 373317031 350339456 420938891 517200 ERX2160150 ERS1883526 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.9552   0.08124   0.67685   0.47578   76   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage Whole Organism All anatomical structures
9828 9828 ERR2102838 ERX2160149 ERS1883525 ERP040145 PRJEB37796 Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E-MTAB-5992 Transcriptome Analysis We wanted to compare gene expression from control untreated zebrafish larvae and 2 mM NaBu treated larvae for 24 hours in order to assess the effect of inhibition of the HDAC pathway in these animals ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2017 08 23|ArrayExpress:E MTAB 5992   Protocols: zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 C3 control RNA SAMEA104224507 Fundacao Champalimaud ENA first public:2017 08 29|ENA last update:2017 08 23|External Id:SAMEA104224507|INSDC center alias:Fundacao Champalimaud|INSDC center name:Fundacao Champalimaud|INSDC first public:2017 08 29T17:02:02Z|INSDC last update:2017 08 23T09:55:35Z|INSDC status:public|Submitter Id:E MTAB 5992:C3 control RNA|age:8|broker name:ArrayExpress|common name:zebrafish|disease:normal|genotype:wild type genotype|sample name:E MTAB 5992:C3 control RNA|strain:AB                 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf E MTAB 5992:C3 control RNA s C3 control RNA s Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf zebrafish were isolated during pharyngula stage daily fed and water changed until 8 dpf 2 mM NaBu for 24 hours in some samples Whole larvae where immersed in RNA later and RNA was extracted using a Qiagen kit following manufacturer recommendations. RNA seq libraries were built using the TruSeq RNA Library Preparation Kit v2 from Illumina RS 122 2001 Experimental Factor: compound:PBS RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina Genome Analyzer IIx   ERP040145 Illumina Genome Analyzer IIx sequencing; Rna seq of control and 2mM NaBu treated zebrafish larvae 8 dpf ENA FIRST PUBLIC:2017 08 29|ENA LAST UPDATE:2018 11 16 C3_R1_all.fastq.gz fastq 1380662008.0 18279108.0 E MTAB 5992:C3 control RNA 0:75.53 1:0 A:345997031;C:338444594;G:316575258;T:379195977;N:449148 75 0     345997031 338444594 316575258 379195977 449148 ERX2160149 ERS1883525 ERA1011308 Fundacao Champalimaud|European Nucleotide Archive Fundacao Champalimaud|European Nucleotide Archive 1 0.95615   0.08131   0.68694   0.45267   74   B   usable mapping rate illumina early_illumina unknown random_priming trueseq bulk unknown unknown   Portugal 2017-08-23 Multi-stage Multi-stage 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");;