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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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr prime5 6 3", "SAMD00028159", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028159", "DRX029568", "Dr prime5 6 3", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3903332800.0, 39033328.0, "DRR032762", "0:100 1:0", "A:1050045822;C:908538410;G:900588661;T:1044116537;N:43370", 100, 0, null, null, 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, null, 0.07976, null, 0.69126, null, 0.46568, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr prime5 6 1", "SAMD00028157", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028157", "DRX029566", "Dr prime5 6 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3863129500.0, 38631295.0, "DRR032760", "0:100 1:0", "A:1035240477;C:901625010;G:895370149;T:1030851937;N:41927", 100, 0, null, null, 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, null, 0.07522, null, 0.69315, null, 0.46516, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr prime25 2", "SAMD00028156", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028156", "DRX029565", "Dr prime25 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3750136100.0, 37501361.0, "DRR032759", "0:100 1:0", "A:1013528040;C:866734984;G:862431819;T:1007403208;N:38049", 100, 0, null, null, 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, null, 0.09079, null, 0.68304, null, 0.47083, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 97 individuals", "Dr bud 2", "SAMD00028154", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028154", "DRX029563", "Dr bud 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 4104778200.0, 41047782.0, "DRR032757", "0:100 1:0", "A:1116316188;C:944738800;G:936257056;T:1107423486;N:42670", 100, 0, null, null, 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, null, 0.10493, null, 0.73407, null, 0.47824, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr bud 1", "SAMD00028153", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028153", "DRX029562", "Dr bud 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 4540291000.0, 45402910.0, "DRR032756", "0:100 1:0", "A:1237914068;C:1042346110;G:1033172731;T:1226799791;N:58300", 100, 0, null, null, 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, null, 0.10478, null, 0.7391, null, 0.46461, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 90epiboly 2", "SAMD00028152", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028152", "DRX029561", "Dr 90epiboly 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3572358600.0, 35723586.0, "DRR032755", "0:100 1:0", "A:971653450;C:821326559;G:816855636;T:962477457;N:45498", 100, 0, null, null, 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, null, 0.10642, null, 0.74213, null, 0.47012, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 90epiboly 1", "SAMD00028151", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028151", "DRX029560", "Dr 90epiboly 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3423980500.0, 34239805.0, "DRR032754", "0:100 1:0", "A:933088185;C:785251613;G:780911148;T:924686406;N:43148", 100, 0, null, null, 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, null, 0.10881, null, 0.74255, null, 0.47068, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 114 individuals", "Dr 8cell 2", "SAMD00028150", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028150", "DRX029559", "Dr 8cell 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3708921900.0, 37089219.0, "DRR032753", "0:100 1:0", "A:985502141;C:874161613;G:869551685;T:979663686;N:42775", 100, 0, null, null, 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, null, 0.02366, null, 0.78896, null, 0.47447, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 96 individuals", "Dr 8cell 1", "SAMD00028149", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028149", "DRX029558", "Dr 8cell 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3666991200.0, 36669912.0, "DRR032752", "0:100 1:0", "A:976118513;C:862559696;G:858017821;T:970254302;N:40868", 100, 0, null, null, 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, null, 0.02403, null, 0.78877, null, 0.46902, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 75epiboly 2", "SAMD00028148", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028148", "DRX029557", "Dr 75epiboly 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3252021500.0, 32520215.0, "DRR032751", "0:100 1:0", "A:885527595;C:746750899;G:742907892;T:876794123;N:40991", 100, 0, null, null, 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, null, 0.10181, null, 0.74862, null, 0.47789, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 75epiboly 1", "SAMD00028147", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028147", "DRX029556", "Dr 75epiboly 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3785053700.0, 37850537.0, "DRR032750", "0:100 1:0", "A:1029014798;C:870946157;G:867537069;T:1017508684;N:46992", 100, 0, null, null, 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, null, 0.10046, null, 0.74921, null, 0.47295, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 72h 2", "SAMD00028146", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028146", "DRX029555", "Dr 72h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3429795800.0, 34297958.0, "DRR032749", "0:100 1:0", "A:928062015;C:792470305;G:786930881;T:922296289;N:36310", 100, 0, null, null, 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, null, 0.09774, null, 0.65437, null, 0.46443, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 72h 1", "SAMD00028145", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028145", "DRX029554", "Dr 72h 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3897194500.0, 38971945.0, "DRR032748", "0:100 1:0", "A:1050989414;C:903225496;G:895783177;T:1047153493;N:42920", 100, 0, null, null, 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, null, 0.09393, null, 0.65486, null, 0.45971, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 6somite 2", "SAMD00028144", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028144", "DRX029553", "Dr 6somite 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3704431000.0, 37044310.0, "DRR032747", "0:100 1:0", "A:1001844161;C:856702913;G:850695568;T:995148798;N:39560", 100, 0, null, null, 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, null, 0.09211, null, 0.72107, null, 0.47195, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 6somite 1", "SAMD00028143", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028143", "DRX029552", "Dr 6somite 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3529311900.0, 35293119.0, "DRR032746", "0:100 1:0", "A:953957996;C:816824469;G:811403696;T:947089530;N:36209", 100, 0, null, null, 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, null, 0.09257, null, 0.72113, null, 0.47004, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 60h 2", "SAMD00028142", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028142", "DRX029551", "Dr 60h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3875337000.0, 38753370.0, "DRR032745", "0:100 1:0", "A:1042558903;C:899892111;G:896867583;T:1035981420;N:36983", 100, 0, null, null, 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, null, 0.09445, null, 0.66156, null, 0.45564, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 5day 3", "SAMD00028140", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028140", "DRX029549", "Dr 5day 3", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3884716000.0, 38847160.0, "DRR032743", "0:100 1:0", "A:1040550584;C:905663425;G:904247323;T:1034215019;N:39649", 100, 0, null, null, 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, null, 0.08287, null, 0.65863, null, 0.47377, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 50 individuals", "Dr 48h 2", "SAMD00028137", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028137", "DRX029546", "Dr 48h 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3702804700.0, 37028047.0, "DRR032740", "0:100 1:0", "A:993931475;C:862403562;G:857808891;T:988623734;N:37038", 100, 0, null, null, 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, null, 0.08526, null, 0.68349, null, 0.45769, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 100 individuals", "Dr 32cell 2", "SAMD00028135", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028135", "DRX029544", "Dr 32cell 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3678713000.0, 36787130.0, "DRR032738", "0:100 1:0", "A:981005900;C:863203049;G:859660640;T:974807835;N:35576", 100, 0, null, null, 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, null, 0.02468, null, 0.77441, null, 0.47485, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [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. 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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.", null, null, "mRNA extracted from pooled embryos of 107 individuals", "Dr 2cell 2", "SAMD00028131", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028131", "DRX029540", "Dr 2cell 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3687517000.0, 36875170.0, "DRR032734", "0:100 1:0", "A:975272080;C:873518282;G:869743434;T:968941851;N:41353", 100, 0, null, null, 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, null, 0.02088, null, 0.81639, null, 0.47553, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 108 individuals", "Dr 2cell 1", "SAMD00028130", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028130", "DRX029539", "Dr 2cell 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 4156651100.0, 41566511.0, "DRR032733", "0:100 1:0", "A:1099943617;C:985498415;G:978884426;T:1092278665;N:45977", 100, 0, null, null, 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, null, 0.02198, null, 0.81197, null, 0.47342, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 80 individuals", "Dr 14somite 3", "SAMD00028129", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028129", "DRX029538", "Dr 14somite 3", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3734610500.0, 37346105.0, "DRR032732", "0:100 1:0", "A:1009418541;C:863710067;G:858061383;T:1003378800;N:41709", 100, 0, null, null, 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, null, 0.08815, null, 0.70816, null, 0.46602, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 80 individuals", "Dr 14somite 2", "SAMD00028128", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028128", "DRX029537", "Dr 14somite 2", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3715174200.0, 37151742.0, "DRR032731", "0:100 1:0", "A:1000703508;C:862290629;G:858173468;T:993968396;N:38199", 100, 0, null, null, 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, null, 0.0819, null, 0.71068, null, 0.46957, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, "mRNA extracted from pooled embryos of 80 individuals", "Dr 14somite 1", "SAMD00028127", null, "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", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing of SAMD00028127", "DRX029536", "Dr 14somite 1", "1", "Total RNA QIAGEN RNeasy followed by TruSeq", null, "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", null, null, null, 3744386000.0, 37443860.0, "DRR032730", "0:100 1:0", "A:1014537326;C:864070910;G:859190201;T:1006549502;N:38061", 100, 0, null, null, 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, null, 0.08957, null, 0.7068, null, 0.47493, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "Japan", "2017-09-20", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"], [25295, "SRR25764045", "SRX21486723", "SRS18719024", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT bud 10 hpf Ribo seq rep1", "GSM7734770", null, "source name:Gastrula|strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT bud 10 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al.  2013] the following options:   outFilterMultimapNmax 1   seedSearchStartLmax 15   outSAMtype BAM SortedByCoordinate   outFilterMismatchNmax 2   alignEndsType EndToEnd   quantMode TranscriptomeSAM   outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Gastrula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Gastrula|developmental stage:Bud 10 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG", "GSM7734770", "GSM7734770: WT bud 10 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734770 r1", "GSM7734770", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_bud_1.fastq.gz", "fastq", 1476985703.0, 55745002.0, "GSM7734770 r1", "0:26.50", "A:266369385;C:466461341;G:473469631;T:270671671;N:13675", 26, null, null, null, 266369385, 466461341, 473469631, 270671671, 13675, "SRX21486723", "SRS18719024", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.773, null, 0.14121, null, 0.82242, null, 0.78464, null, 30, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [25296, "SRR25764046", "SRX21486722", "SRS18719023", "SRP457105", "PRJNA1009809", "Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [Ribo Seq]", "GSE241753", "Other", "Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points  namelyat the 256 cell 2.5 hpf  1000 cell 3 hpf  sphere 4 hpf  shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis  polysome profiling  ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis.", "parent bioproject:PRJNA1009800", "pubmed:39402326", null, "WT sphere 4 hpf Ribo seq rep1", "GSM7734769", null, "source name:Blastula|strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG|geo loc name:missing|collection date:missing", "WT sphere 4 hpf Ribo seq rep1", "We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  short 20 23 nt and long 28 33 nt ribosome footprints were analyzed separately. rRNA filtered reads were aligned to GRCz11.108 using STAR v2.6.1c [Dobin et al.  2013] the following options:   outFilterMultimapNmax 1   seedSearchStartLmax 15   outSAMtype BAM SortedByCoordinate   outFilterMismatchNmax 2   alignEndsType EndToEnd   quantMode TranscriptomeSAM   outSAMattributes NH HI AS nM NM MD We identified the A site location in each mapped read with Scikit ribo [Fang et al. 2018]  which uses a random forest with recursive feature selection and a generalized linear model for accurate A site prediction based on matched ribosome profiling and RNA Seq datasets. Kallisto 0.44.0 with parameters  b 100   single  l 180  s 20  t 40 was used to quantify transcript abundances in Transcripts Per Million TPM from RNA Seq data based on the reference set of MANE annotated transcripts see Codon usage analysis for description of this annotation. To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms  all RNAfold dependencies in Scikit ribo were omitted  and the index was built separately for each chromosome. To make the GRCz11 GTF compatible with Scikit ribo  transcript/UTR annotations were removed. For each transcript  the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates  taking into account the gene strand. To estimate codon dwell times  we utilised ribosome footprints with length 30 34 nt. Assembly: GRCz11 Supplementary files format and content: csv; codon dwell times from scikit ribo for all samples Supplementary files format and content: csv; transcript per million TPM counts per transcript in MANE annotation Library strategy: Ribo Seq", "Blastula", "unperturbed growth conditions in E3 medium for zebrafish embryos.", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their 5\u2019 ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", "Embryos were grown in standard housing conditions namely28\u00b0C at a 14/10 hour light/dark cycle.", "strain:TLAB strain|tissue:Blastula|developmental stage:Sphere 4 hpf|treatment:100 \u00b5g/ml CHX  100 \u00b5g/ml TIG", "GSM7734769", "GSM7734769: WT sphere 4 hpf Ribo seq rep1; Danio rerio; OTHER", "GSM7734769 r1", "GSM7734769", "1", "200 whole embryos were flash frozen in liquid nitrogen and subsequently lysed in footprint lysis buffer containing 100 \u00b5g/ml CHX and 100 \u00b5g/ml TIG  0.1% NP 40  10 \u00b5g/ml aprotinin  20 \u00b5M leupeptin  2.5 \u00b5M pepstatin A  0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously  triturated through a 26G gauge needle  and spun down for 7 minutes at 16 000xg/ 4\u00b0C. Supernatant was transferred to a new tube. 20 \u00b5g RNA in 200 \u00b5l polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2 000 rpm/22\u00b0C. post incubation on ice for 5 minutes  extracts were pre cleared by centrifugation for 5 minutes at 3 000 g/ 4\u00b0C. Ribosomes were pelleted through 3 ml of a sucrose cushion 1 M sucrose  20 mM Tris pH=8.0  140 mM KCl  5 mM MgCl2  1 mM DTT by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50 000 rpm/ 4\u00b0C. Ribosome pellets were rinsed once  dissolved in 200 \u00b5l drug free polysome lysis buffer  and incubated with 200 U hiPSC or 300 U NPC RNase I for 45 minutes at 2 000 rpm/22\u00b0C. Ribosome footprint libraries were prepared essentially as described McGlincy and Ingolia  2017; Wu 2019 with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 \u00b5l LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection  with T4 PNK and ligated to pre adenylated adapters containing 5 random nucleotides at their five prime ends McGlinzy 2017 with T4 RNA Ligase 2  truncated KQ. Adapter ligated RNA was subjected to rRNA depletion using the Ribo Seq riboPOOL h/m/r depletion kit siTOOLs for CHX only samples  and legacy RiboZero Gold kit Illumina for CHX+TIG samples The rRNA depleted footprints were reverse transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 commercially available as CircLigase. Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single end sequencing was performed on a NextSeq 500 platform Illumina.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP457105", null, null, "WT_ribo_sphere_1.fastq.gz", "fastq", 1336027898.0, 47907512.0, "GSM7734769 r1", "0:27.89", "A:229038284;C:439455963;G:429428292;T:238088512;N:16847", 27, null, null, null, 229038284, 439455963, 429428292, 238088512, 16847, "SRX21486722", "SRS18719023", "SRA1700409", "Mechanisms of Protein Biogenesis, Max Planck Institute for Biochemistry", "Max Planck Institute of Biochemistry", 1, 0.85867, null, 0.20418, null, 0.8776, null, 0.79481, null, 24, null, "B", null, "usable mapping rate", "illumina", "nextseq", "5prime", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Germany", "2023-08-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [35567, "SRR32928199", "SRX28203119", "SRS24552825", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 6", "100", "100", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.F01.fq.gz", "fastq", 800436.0, 9529.0, "expt2.broad.48.enzymatic.P01.F01.fq.gz", "0:84", "A:247920;C:168170;G:180799;T:203153;N:394", 84, null, null, null, 247920, 168170, 180799, 203153, 394, "SRX28203119", "SRS24552825", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35568, "SRR32928200", "SRX28203118", "SRS24552823", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 5", "99", "99", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.E01.fq.gz", "fastq", 496356.0, 5909.0, "expt2.broad.48.enzymatic.P01.E01.fq.gz", "0:84", "A:156600;C:99183;G:113282;T:127036;N:255", 84, null, null, null, 156600, 99183, 113282, 127036, 255, "SRX28203118", "SRS24552823", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35569, "SRR32928201", "SRX28203117", "SRS24552824", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 4", "98", "98", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.D01.fq.gz", "fastq", 2053800.0, 24450.0, "expt2.broad.48.enzymatic.P01.D01.fq.gz", "0:84", "A:668634;C:393806;G:431279;T:559022;N:1059", 84, null, null, null, 668634, 393806, 431279, 559022, 1059, "SRX28203117", "SRS24552824", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35570, "SRR32928202", "SRX28203116", "SRS24552821", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 3", "97", "97", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.C01.fq.gz", "fastq", 2159052.0, 25703.0, "expt2.broad.48.enzymatic.P01.C01.fq.gz", "0:84", "A:837784;C:348085;G:463530;T:508544;N:1109", 84, null, null, null, 837784, 348085, 463530, 508544, 1109, "SRX28203116", "SRS24552821", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35571, "SRR32928203", "SRX28203115", "SRS24552822", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.B01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 2", "96", "96", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.B01.fq.gz", "fastq", 3287508.0, 39137.0, "expt2.broad.48.enzymatic.P01.B01.fq.gz", "0:84", "A:1090202;C:644484;G:702124;T:848812;N:1886", 84, null, null, null, 1090202, 644484, 702124, 848812, 1886, "SRX28203115", "SRS24552822", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35572, "SRR32928204", "SRX28203114", "SRS24552819", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using enzymatic digestion. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.enzymatic.P01.A01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  enzymatic dissociation  replicate 1", "95", "95", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.enzymatic.P01.A01.fq.gz", "fastq", 6623400.0, 78850.0, "expt2.broad.48.enzymatic.P01.A01.fq.gz", "0:84", "A:2915935;C:1012732;G:1256523;T:1434621;N:3589", 84, null, null, null, 2915935, 1012732, 1256523, 1434621, 3589, "SRX28203114", "SRS24552819", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35573, "SRR32928205", "SRX28203113", "SRS24552820", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.bead.P18.H02.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:16|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  bead dissociation  replicate 16", "94", "94", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. Cell IDs are in the header of each fastq.", null, null, "OTHER", "TRANSCRIPTOMIC SINGLE CELL", "other", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP575522", null, null, "expt2.broad.48.bead.P18.H02.fq.gz", "fastq", 18079152.0, 215228.0, "expt2.broad.48.bead.P18.H02.fq.gz", "0:84", "A:6013555;C:3409380;G:3853431;T:4793252;N:9534", 84, null, null, null, 6013555, 3409380, 3853431, 4793252, 9534, "SRX28203113", "SRS24552820", "SRA2104467", "University of Washington|Genome Sciences", "University of Washington", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "other", "unknown", "sc", "single_cell_generic", "generic-scrnaseq-only", null, "United States", "2025-03-31", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [35574, "SRR32928206", "SRX28203112", "SRS24552818", "SRP575522", "PRJNA1244443", "An improved  high yield method for isolating nuclei from individual zebrafish embryos for single nucleus RNA sequencing", "PRJNA1244443", "Other", "Zebrafish are an ideal system to study the effects of chemical  genetic  and environmental perturbations on development due to their high fecundity and fast growth. Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.bead.P18.H01.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:15|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  bead dissociation  replicate 15", "93", "93", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 48hpf whole zebrafish embryo dissociated using bead homogenization. This subpool was sequenced on a large number of cells in order to determine the cell number and diversity captured by the method.", null, "expt2.broad.48.bead.P18.G02.fq.gz", null, "seq depth:broad many cells|Experiment id:2|dissociation method:bead|replicate:14|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:48 hpf|dev stage:48 hpf|collection date:2024 01 31|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt2  broad sequencing of many cells at low depth  48hpf  bead dissociation  replicate 14", "92", "92", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. Each fasta represents a sample split from a large multiplexed sequencing run. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.G12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 7", "212", "212", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.F12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 6", "211", "211", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.H3.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:22|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 22", "22", "22", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.E12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 5", "210", "210", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.D12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 4", "209", "209", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.C12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 3", "208", "208", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.B12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:2|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 2", "207", "207", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using enzymatic digestion.", null, "expt3.96.enzymatic.P18.A12.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:enzymatic|replicate:1|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  enzymatic dissociation  replicate 1", "206", "206", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.H11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:8|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 8", "205", "205", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.G11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:7|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 7", "204", "204", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.F11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:6|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 6", "203", "203", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.E11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:5|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 5", "202", "202", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Recently  single cell sequencing has emerged as a powerful tool to measure the effect of these perturbations at a whole embryo scale. These types of experiments rely on the ability to isolate nuclei from a large number of individually barcoded zebrafish embryos in parallel. Here we report a method for efficiently isolating high quality nuclei from zebrafish embryos in a 96 well plate format by bead homogenization in a lysis buffer. Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.D11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:4|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 4", "201", "201", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.G5.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:21|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 21", "21", "21", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 12hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt1.12.bead.P1.A5.fq.gz", null, "seq depth:NA|Experiment id:1|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:12 hpf|dev stage:8 somite|collection date:2024 03 08|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt1  12hpf  bead dissociation  replicate 3", "3", "3", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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Through head to head sciPlex RNA seq experiments  we demonstrate that this method represents a substantial improvement over enzymatic dissociation and that it is compatible with a wide range of developmental stages.", null, null, "Sci plexRNAseq of a 96hpf whole zebrafish embryo dissociated using bead homogenization.", null, "expt3.96.bead.P18.C11.fq.gz", null, "seq depth:NA|Experiment id:3|dissociation method:bead|replicate:3|strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:96 hpf|dev stage:96 hpf|collection date:2024 03 19|geo loc name:USA:Washington  Seattle|sex:not collected|tissue:Whole Embryo|sample type:Whole organism|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "sciPlex RNAseq of whole Danio rerio embryos: expt3  96hpf  bead dissociation  replicate 3", "200", "200", "Libraries were generated using sciPlex RNAseq3 combinatorial indexing. 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