{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"unspecified\" and tissue_curation = \"Whole Organism\"", "rows": [[36761, "SRR10295266", "SRX7008094", "SRS431105", "SRP023492", "PRJNA206070", "Nanog  SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal to zygotic transition", "GSE47558", "Other", "Upon fertilization  maternal factors direct development in a transcriptionally silent embryo. At the maternal to zygotic transition MZT  a universal step in animal development  unknown maternal factors trigger zygotic genome activation ZGA. In zebrafish  ZGA is required for gastrulation and clearance of maternal mRNAs  which is achieved in part by the conserved microRNA miR 430. However  the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog  Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors  thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre MZT embryo revealed that nanog  sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog  SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation  and a failure to activate >75% of zygotic genes. Furthermore  we found that Nanog binds the miR 430 locus and together with Pou5f1 and SoxB1 initiate miR 430 expression and activity. Our results demonstrate that maternal Nanog  Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR 430 expression. Overall design: Wild type and loss of function total mRNA sequencing of embryonic transcriptomes pre  and post MZT; ribosome profiling pre MZT", null, "pubmed:24056933", null, "WT 2hpf Total mRNA", "GSM1152440", null, "source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA", null, null, null, null, null, null, null, null, "WT 64c R0", "AGR000324", "AGR000324", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP023492", null, null, "AGR000324_R1.fastq.gz", "fastq", 781504124.0, 10282949.0, "AGR000324 R1.fastq.gz", "0:76", "A:151879560;C:240178928;G:220957551;T:168456166;N:31919", 76, null, null, null, 151879560, 240178928, 220957551, 168456166, 31919, "SRX7008094", "SRS431105", "SRA980383", "Yale_Giraldez|Genetics", "Giraldez Lab, Genetics, Yale University", 1, 0.88875, null, 0.14141, null, 0.796, null, 0.72154, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-10-16", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [39687, "SRR2051113", "SRX1048368", "SRS952733", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P39", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 4", "P39", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P39_EL4517_GATCAG_L001_R1_001.fastq.gz P39_EL4517_GATCAG_L002_R1_001.fastq.gz P39_EL4517_GATCAG_L007_R1_001.fastq.gz P39_EL4517_GATCAG_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4090297192.0, 40497992.0, "P39", "0:101", "A:1016157993;C:993771683;G:965986507;T:1113686588;N:694421", 101, null, null, null, 1016157993, 993771683, 965986507, 1113686588, 694421, "SRX1048368", "SRS952733", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9417, null, 0.14428, null, 0.68937, null, 0.5438, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39688, "SRR2051110", "SRX1048367", "SRS952731", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P37", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 3", "P37", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P37_EL4516_ACTTGA_L008_R1_001.fastq.gz P37_EL4516_ACTTGA_L007_R1_001.fastq.gz P37_EL4516_ACTTGA_L002_R1_001.fastq.gz P37_EL4516_ACTTGA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4647442886.0, 46014286.0, "P37", "0:101", "A:1149955739;C:1129088798;G:1093234722;T:1274375148;N:788479", 101, null, null, null, 1149955739, 1129088798, 1093234722, 1274375148, 788479, "SRX1048367", "SRS952731", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94585, null, 0.12571, null, 0.68633, null, 0.52597, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39689, "SRR2051112", "SRX1048366", "SRS952732", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P36", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 2", "P36", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P36_EL4527_CCGTCC_L008_R1_001.fastq.gz P36_EL4527_CCGTCC_L007_R1_001.fastq.gz P36_EL4527_CCGTCC_L002_R1_001.fastq.gz P36_EL4527_CCGTCC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4296894611.0, 42543511.0, "P36", "0:101", "A:1050039699;C:1061123166;G:1022913715;T:1162094624;N:723407", 101, null, null, null, 1050039699, 1061123166, 1022913715, 1162094624, 723407, "SRX1048366", "SRS952732", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94977, null, 0.13188, null, 0.70976, null, 0.52728, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39690, "SRR2051109", "SRX1048365", "SRS952730", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P35", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 3.0 uM CPO Rep 1", "P35", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P35_EL4526_ATGTCA_L008_R1_001.fastq.gz P35_EL4526_ATGTCA_L007_R1_001.fastq.gz P35_EL4526_ATGTCA_L002_R1_001.fastq.gz P35_EL4526_ATGTCA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4094752706.0, 40542106.0, "P35", "0:101", "A:1009779802;C:1004374749;G:969241794;T:1110655194;N:701167", 101, null, null, null, 1009779802, 1004374749, 969241794, 1110655194, 701167, "SRX1048365", "SRS952730", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94442, null, 0.13203, null, 0.70023, null, 0.53953, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39691, "SRR2051102", "SRX1048364", "SRS952729", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P29", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 4", "P29", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P29_EL4510_CTTGTA_L008_R1_001.fastq.gz P29_EL4510_CTTGTA_L007_R1_001.fastq.gz P29_EL4510_CTTGTA_L002_R1_001.fastq.gz P29_EL4510_CTTGTA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4983571896.0, 49342296.0, "P29", "0:101", "A:1247122516;C:1202173111;G:1173654831;T:1359775597;N:845841", 101, null, null, null, 1247122516, 1202173111, 1173654831, 1359775597, 845841, "SRX1048364", "SRS952729", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94329, null, 0.13234, null, 0.68286, null, 0.51586, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39692, "SRR2051100", "SRX1048363", "SRS952727", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P28", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 3", "P28", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P28_EL4509_CAGATC_L008_R1_001.fastq.gz P28_EL4509_CAGATC_L007_R1_001.fastq.gz P28_EL4509_CAGATC_L002_R1_001.fastq.gz P28_EL4509_CAGATC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4032678914.0, 39927514.0, "P28", "0:101", "A:1015356577;C:970369004;G:937306142;T:1108957703;N:689488", 101, null, null, null, 1015356577, 970369004, 937306142, 1108957703, 689488, "SRX1048363", "SRS952727", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.93887, null, 0.13869, null, 0.69079, null, 0.52237, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39693, "SRR2051101", "SRX1048362", "SRS952728", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P26", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 2", "P26", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P26_EL4508_GCCAAT_L001_R1_001.fastq.gz P26_EL4508_GCCAAT_L007_R1_001.fastq.gz P26_EL4508_GCCAAT_L008_R1_001.fastq.gz P26_EL4508_GCCAAT_L002_R1_001.fastq.gz", "fastq fastq fastq fastq", 6526758875.0, 64621375.0, "P26", "0:101", "A:1635664768;C:1568967965;G:1518148006;T:1802863908;N:1114228", 101, null, null, null, 1635664768, 1568967965, 1518148006, 1802863908, 1114228, "SRX1048362", "SRS952728", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.93822, null, 0.15203, null, 0.68609, null, 0.53171, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39694, "SRR2051096", "SRX1048361", "SRS952726", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P25", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 1.0 uM CPO Rep 1", "P25", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P25_EL4511_ATCACG_L001_R1_001.fastq.gz P25_EL4511_ATCACG_L002_R1_001.fastq.gz P25_EL4511_ATCACG_L007_R1_001.fastq.gz P25_EL4511_ATCACG_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4185957322.0, 41445122.0, "P25", "0:101", "A:1081936223;C:978799105;G:956795307;T:1167714259;N:712428", 101, null, null, null, 1081936223, 978799105, 956795307, 1167714259, 712428, "SRX1048361", "SRS952726", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9288, null, 0.17032, null, 0.6801, null, 0.51298, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39695, "SRR2051095", "SRX1048360", "SRS952725", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P19", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 4", "P19", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P19_EL4521_GGCTAC_L008_R1_001.fastq.gz P19_EL4521_GGCTAC_L007_R1_001.fastq.gz P19_EL4521_GGCTAC_L002_R1_001.fastq.gz P19_EL4521_GGCTAC_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4293546461.0, 42510361.0, "P19", "0:101", "A:1062707728;C:1045602693;G:1011860446;T:1172670772;N:704822", 101, null, null, null, 1062707728, 1045602693, 1011860446, 1172670772, 704822, "SRX1048360", "SRS952725", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94381, null, 0.13697, null, 0.69051, null, 0.51415, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39696, "SRR2051094", "SRX1048359", "SRS952724", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P18", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 3", "P18", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P18_EL4520_TAGCTT_L008_R1_001.fastq.gz P18_EL4520_TAGCTT_L007_R1_001.fastq.gz P18_EL4520_TAGCTT_L002_R1_001.fastq.gz P18_EL4520_TAGCTT_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4257944163.0, 42157863.0, "P18", "0:101", "A:1044532409;C:1049992329;G:1010166097;T:1152524203;N:729125", 101, null, null, null, 1044532409, 1049992329, 1010166097, 1152524203, 729125, "SRX1048359", "SRS952724", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94262, null, 0.14592, null, 0.69014, null, 0.52498, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39697, "SRR2051093", "SRX1048358", "SRS952723", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P17", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 2", "P17", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P17_EL4522_AGTCAA_L007_R1_001.fastq.gz P17_EL4522_AGTCAA_L008_R1_001.fastq.gz P17_EL4522_AGTCAA_L002_R1_001.fastq.gz P17_EL4522_AGTCAA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4278385553.0, 42360253.0, "P17", "0:101", "A:1040955882;C:1060023973;G:1019487833;T:1157186726;N:731139", 101, null, null, null, 1040955882, 1060023973, 1019487833, 1157186726, 731139, "SRX1048358", "SRS952723", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94697, null, 0.14458, null, 0.69643, null, 0.53451, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39698, "SRR2051092", "SRX1048357", "SRS952722", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "P15", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP 0.1 uM CPO Rep 1", "P15", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "P15_EL4523_AGTTCC_L001_R1_001.fastq.gz P15_EL4523_AGTTCC_L002_R1_001.fastq.gz P15_EL4523_AGTTCC_L007_R1_001.fastq.gz P15_EL4523_AGTTCC_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4341747499.0, 42987599.0, "P15", "0:101", "A:1052621077;C:1088380866;G:1041958433;T:1158051746;N:735377", 101, null, null, null, 1052621077, 1088380866, 1041958433, 1158051746, 735377, "SRX1048357", "SRS952722", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94563, null, 0.153, null, 0.69822, null, 0.54133, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-06-04", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39699, "SRR2051091", "SRX1048356", "SRS952721", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN9", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 4", "CN9", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "CN9_EL4515_TTAGGC_L001_R1_001.fastq.gz CN9_EL4515_TTAGGC_L002_R1_001.fastq.gz CN9_EL4515_TTAGGC_L007_R1_001.fastq.gz CN9_EL4515_TTAGGC_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4220387212.0, 41786012.0, "CN9", "0:101", "A:1031722430;C:1044497851;G:1005706674;T:1137783022;N:677235", 101, null, null, null, 1031722430, 1044497851, 1005706674, 1137783022, 677235, "SRX1048356", "SRS952721", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.95231, null, 0.14084, null, 0.69682, null, 0.52966, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39700, "SRR2051090", "SRX1048354", "SRS952719", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN8", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 3", "CN8", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "CN8_EL4505_CGATGT_L008_R1_001.fastq.gz CN8_EL4505_CGATGT_L007_R1_001.fastq.gz CN8_EL4505_CGATGT_L002_R1_001.fastq.gz CN8_EL4505_CGATGT_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 5835502553.0, 57777253.0, "CN8", "0:101", "A:1424369529;C:1441755207;G:1391851806;T:1576540272;N:985739", 101, null, null, null, 1424369529, 1441755207, 1391851806, 1576540272, 985739, "SRX1048354", "SRS952719", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94643, null, 0.12925, null, 0.70725, null, 0.52949, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39701, "SRR2050894", "SRX1048353", "SRS952718", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN7", null, "breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 2", "CN7", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "CN7_EL4507_ACAGTG_L008_R1_001.fastq.gz CN7_EL4507_ACAGTG_L007_R1_001.fastq.gz CN7_EL4507_ACAGTG_L002_R1_001.fastq.gz CN7_EL4507_ACAGTG_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 4789094477.0, 47416777.0, "CN7", "0:101", "A:1160528098;C:1197558725;G:1155573375;T:1274638263;N:796016", 101, null, null, null, 1160528098, 1197558725, 1155573375, 1274638263, 796016, "SRX1048353", "SRS952718", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.9501, null, 0.14828, null, 0.69966, null, 0.52764, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39702, "SRR2050892", "SRX1048352", "SRS952717", "SRP059060", "PRJNA285816", "Danio rerio Raw sequence reads", "PRJNA285816", "Whole Genome Sequencing", "Here we have generated and validated zebrafish models for mild  moderate and severe acute organophosphorus poisoning by exposing zebrafish larvae to different concentrations of the prototypic OP compound  chlorpyrifos oxon. Our results show that zebrafish models mimic most of the aspects of this toxidrome in humans  including acetylcholinesterase inhibition  NMDA receptor activation  calcium dysregulation and inflammatory and immune response.", null, null, null, null, "CN5", null, "breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D. rerio OP Control Rep 1", "CN5", "CN5 EL4506 TGACCA", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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>", "SRP059060", null, null, "CN5_EL4506_TGACCA_L001_R1_001.fastq.gz CN5_EL4506_TGACCA_L002_R1_001.fastq.gz CN5_EL4506_TGACCA_L007_R1_001.fastq.gz CN5_EL4506_TGACCA_L008_R1_001.fastq.gz", "fastq fastq fastq fastq", 4526144512.0, 44813312.0, "CN5", "0:101", "A:1109966549;C:1116619353;G:1075422479;T:1223366972;N:769159", 101, null, null, null, 1109966549, 1116619353, 1075422479, 1223366972, 769159, "SRX1048352", "SRS952717", "SRA271167", "Mississippi State University|IGBB", "US Army ERDC", 1, 0.94604, null, 0.14084, null, 0.69004, null, 0.53407, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-03-17", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52829, "SRR9277355", "SRX6047142", "SRS4950160", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample04", null, "dkc1 elu1 mut1", null, "isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "MUT1", "MUT1", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "MUT-1_R1.fastq.gz", "fastq", 2425739178.0, 32540543.0, "MUT 1 R1.fastq.gz", "0:74.55 1:0", "A:562954867;C:599474858;G:575980257;T:687194946;N:134250", 74, 0, null, null, 562954867, 599474858, 575980257, 687194946, 134250, "SRX6047142", "SRS4950160", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.96592, null, 0.05193, null, 0.69181, null, 0.46287, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52830, "SRR9277356", "SRX6047141", "SRS4950159", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample03", null, "dkc1 elu1 sib3", null, "isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "SIB3", "SIB3", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "SIB-3_R1.fastq.gz", "fastq", 2525161946.0, 33921476.0, "SIB 3 R1.fastq.gz", "0:74.44 1:0", "A:617606365;C:576906982;G:574368411;T:756144418;N:135770", 74, 0, null, null, 617606365, 576906982, 574368411, 756144418, 135770, "SRX6047141", "SRS4950159", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.95481, null, 0.09246, null, 0.70187, null, 0.48651, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52831, "SRR9277357", "SRX6047140", "SRS4950158", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample02", null, "dkc1 elu1 sib2", null, "isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "SIB2", "SIB2", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "SIB-2_R1.fastq.gz", "fastq", 2500753589.0, 33594139.0, "SIB 2 R1.fastq.gz", "0:74.44 1:0", "A:594107753;C:588927623;G:585955773;T:731305179;N:457261", 74, 0, null, null, 594107753, 588927623, 585955773, 731305179, 457261, "SRX6047140", "SRS4950158", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.95785, null, 0.07623, null, 0.70512, null, 0.49187, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52832, "SRR9277358", "SRX6047139", "SRS4950157", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample01", null, "dkc1 elu1 sib1", null, "isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "SIB1", "SIB1", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "SIB-1_R1.fastq.gz", "fastq", 2611643150.0, 35032800.0, "SIB 1 R1.fastq.gz", "0:74.55 1:0", "A:594796815;C:658132193;G:620365621;T:738201586;N:146935", 74, 0, null, null, 594796815, 658132193, 620365621, 738201586, 146935, "SRX6047139", "SRS4950157", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.97084, null, 0.05106, null, 0.69858, null, 0.46901, null, 73, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52833, "SRR9277359", "SRX6047138", "SRS4950156", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample06", null, "dkc1 elu1 mut3", null, "isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "MUT3", "MUT3", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "MUT-3_R1.fastq.gz", "fastq", 2503783299.0, 33623629.0, "MUT 3 R1.fastq.gz", "0:74.46 1:0", "A:603400760;C:568138093;G:589455352;T:742564020;N:225074", 74, 0, null, null, 603400760, 568138093, 589455352, 742564020, 225074, "SRX6047138", "SRS4950156", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.95328, null, 0.08246, null, 0.69581, null, 0.48805, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [52834, "SRR9277360", "SRX6047137", "SRS4950155", "SRP201168", "PRJNA548449", "Dyskerin impairment in zebrafish", "PRJNA548449", "Other", "One of the most important post transcriptional modification of RNA molecules in eukaryotic cells is pseudouridylation catalyzed by the multifunctional dyskerin enzyme. Interestingly  despite its abundance and importance  we still know very little about the role of this modification during cell function. This transcriptomic dataset contains three biological replicates from 36 hpf dyskerin loss of function homozygous zebrafish embryos and their siblings.", null, null, "sample05", null, "dkc1 elu1 mut2", null, "isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 36hpf", "MUT2", "MUT2", "Total RNA was extracted from whole zebrafish embryos at 36hpf  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. Our samples were sequenced with Illumina technology by Microsynth Microsynth AG  Switzerland according to standard llumina protocols.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP201168", null, null, "MUT-2_R1.fastq.gz", "fastq", 2437701211.0, 32733070.0, "MUT 2 R1.fastq.gz", "0:74.47 1:0", "A:590961375;C:565727869;G:562583560;T:718173630;N:254777", 74, 0, null, null, 590961375, 565727869, 562583560, 718173630, 254777, "SRX6047137", "SRS4950155", "SRA897402", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 1, 0.95589, null, 0.07601, null, 0.70317, null, 0.49704, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2019-06-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [54188, "SRR10095964", "SRX6828145", "SRS5370320", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "5b", null, "strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "5b", "5b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "loader:latf load", "olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 90080193105.0, 566542095.0, "5b.gz", "0:26 1:133", "A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734", 26, 133, null, null, 25143336916, 20071432223, 20537826191, 24313961041, 13636734, "SRX6828145", "SRS5370320", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.00976, 0.95301, 0.00215, 0.10077, 0.97926, 0.77851, 0.44407, 0.5221, 26, 133, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [54189, "SRR10095965", "SRX6828144", "SRS5370319", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "5a", null, "strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "5a", "5a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "loader:latf load", "olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 106640540616.0, 670695224.0, "5a.gz", "0:26 1:133", "A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145", 26, 133, null, null, 29532468637, 23968826821, 24791831474, 28331248539, 16165145, "SRX6828144", "SRS5370319", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.01014, 0.95016, 0.00222, 0.09527, 0.97855, 0.78212, 0.41929, 0.50263, 26, 133, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [54190, "SRR10095966", "SRX6828143", "SRS5370318", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "2b", null, "strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "2b", "2b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "loader:latf load", "olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 100194025377.0, 630151103.0, "2b.gz", "0:26 1:133", "A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462", 26, 133, null, null, 27235389395, 22388810842, 23041272930, 27513445748, 15106462, "SRX6828143", "SRS5370318", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.0127, 0.95456, 0.00215, 0.09469, 0.97463, 0.79308, 0.43287, 0.50046, 26, 133, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [54191, "SRR10095967", "SRX6828142", "SRS5370317", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "2a", null, "strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "2a", "2a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP221273", null, "loader:latf load", "2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq", 30654488793.0, 192795527.0, "2a.gz", "0:26 1:133", "A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245", 26, 133, null, null, 8922702024, 6370087682, 7321183700, 8019014142, 21501245, "SRX6828142", "SRS5370317", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.00427, 0.91705, 0.00106, 0.08701, 0.98999, 0.8198, 0.35255, 0.50555, 26, 133, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [54192, "SRR10095968", "SRX6828141", "SRS5370316", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis  to launch an effort to define the diversity of cell types during zebrafish organogenesis  and to examine the transcriptional profiles that produce each cell type over developmental time.", null, null, null, null, "1b", null, "strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "1b", "1b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "loader:latf load", "olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 98193351273.0, 617568247.0, "1b.gz", "0:26 1:133", "A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797", 26, 133, null, null, 27237053473, 21828277485, 22951157364, 26162156154, 14706797, "SRX6828141", "SRS5370316", "SRA960102", "University of Oregon|Institute of Neuroscience", "University of Oregon", 2, 0.01479, 0.95138, 0.00273, 0.12104, 0.97327, 0.78293, 0.39405, 0.4998, 26, 133, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-12-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [54193, "SRR10095969", "SRX6828140", "SRS5370315", "SRP221273", "PRJNA564810", "A Single Cell Transcriptome Atlas for Zebrafish Development", "PRJNA564810", "Other", "The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge  we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap  we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore  we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes  including those that are currently known only by sequence and/or that lack expression information altogether. 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"/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "unspecified", "label": "unspecified", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "Larval", "label": "Larval", "count": 36, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&devstage_curation_coarse=Larval", 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&devstage_curation=Hatching", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&devstage_curation=Pharyngula", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&devstage_curation=Cleavage", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified&tissue_curation=Whole+Organism", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 41, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=unspecified", "selected": true}], 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