rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,,pubmed:24056933,,WT 2hpf Total mRNA,GSM1152440,,source name:WT 2hpf Total mRNA|tissue:Whole embryos|strain:TUAB|Stage:2hpf|treatment:n1|rna subtype:total RNA,,,,,,,,,WT 64c R0,AGR000324,AGR000324,RNA,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP023492,,,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,,,,151879560,240178928,220957551,168456166,31919,SRX7008094,SRS431105,SRA980383,Yale_Giraldez|Genetics,"Giraldez Lab, Genetics, Yale University",1,0.88875,,0.14141,,0.796,,0.72154,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,small_rna,unknown,bulk,unknown,unknown,,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.,,,,,P39,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 4,P39,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1016157993,993771683,965986507,1113686588,694421,SRX1048368,SRS952733,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9417,,0.14428,,0.68937,,0.5438,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P37,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 3,P37,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1149955739,1129088798,1093234722,1274375148,788479,SRX1048367,SRS952731,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94585,,0.12571,,0.68633,,0.52597,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P36,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 2,P36,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1050039699,1061123166,1022913715,1162094624,723407,SRX1048366,SRS952732,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94977,,0.13188,,0.70976,,0.52728,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P35,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Severe phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 3.0 uM CPO Rep 1,P35,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1009779802,1004374749,969241794,1110655194,701167,SRX1048365,SRS952730,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94442,,0.13203,,0.70023,,0.53953,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P29,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 4,P29,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1247122516,1202173111,1173654831,1359775597,845841,SRX1048364,SRS952729,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94329,,0.13234,,0.68286,,0.51586,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P28,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 3,P28,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1015356577,970369004,937306142,1108957703,689488,SRX1048363,SRS952727,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93887,,0.13869,,0.69079,,0.52237,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P26,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 2,P26,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1635664768,1568967965,1518148006,1802863908,1114228,SRX1048362,SRS952728,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.93822,,0.15203,,0.68609,,0.53171,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P25,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Moderate phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 1.0 uM CPO Rep 1,P25,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1081936223,978799105,956795307,1167714259,712428,SRX1048361,SRS952726,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9288,,0.17032,,0.6801,,0.51298,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P19,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 4,P19,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1062707728,1045602693,1011860446,1172670772,704822,SRX1048360,SRS952725,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94381,,0.13697,,0.69051,,0.51415,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P18,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 3,P18,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1044532409,1049992329,1010166097,1152524203,729125,SRX1048359,SRS952724,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94262,,0.14592,,0.69014,,0.52498,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P17,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 2,P17,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1040955882,1060023973,1019487833,1157186726,731139,SRX1048358,SRS952723,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94697,,0.14458,,0.69643,,0.53451,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,P15,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:mild phenotype|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP 0.1 uM CPO Rep 1,P15,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1052621077,1088380866,1041958433,1158051746,735377,SRX1048357,SRS952722,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94563,,0.153,,0.69822,,0.54133,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,CN9,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 4,CN9,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1031722430,1044497851,1005706674,1137783022,677235,SRX1048356,SRS952721,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.95231,,0.14084,,0.69682,,0.52966,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,CN8,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 3,CN8,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1424369529,1441755207,1391851806,1576540272,985739,SRX1048354,SRS952719,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94643,,0.12925,,0.70725,,0.52949,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,CN7,,breed:Wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 2,CN7,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1160528098,1197558725,1155573375,1274638263,796016,SRX1048353,SRS952718,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.9501,,0.14828,,0.69966,,0.52764,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,CN5,,breed:wild type|dev stage:larvae|sex:not applicable|tissue:whole organism|treatment:Control|BioSampleModel:Model organism or animal,,,,,,,,,D. rerio OP Control Rep 1,CN5,CN5 EL4506 TGACCA,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 2500,1010Application ReadForward1,SRP059060,,,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,,,,1109966549,1116619353,1075422479,1223366972,769159,SRX1048352,SRS952717,SRA271167,Mississippi State University|IGBB,US Army ERDC,1,0.94604,,0.14084,,0.69004,,0.53407,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-03-17,Larval,Larval,Whole Organism,All anatomical structures
39751,SRR2422954,SRX1092140,SRS987764,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFAB KD,U2AFA2B KD,U2A2FA and U2AF2B knockdown,,treatment:U2AF2A B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2A and U2AF2B KD,U2AFAB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_2_2.fastq.gz zebrafish_U2af2KD_2_1.fastq.gz,fastq fastq,4010033906.0,19851653.0,u2afa u2afb kd,0:101 1:101,A:954988404;C:1049486839;G:1028325376;T:975960838;N:1272449,101,101,,,954988404,1049486839,1028325376,975960838,1272449,SRX1092140,SRS987764,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88891,0.88704,0.22441,0.2245,0.73781,0.74111,0.60755,0.61314,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39752,SRR2422968,SRX1092139,SRS987762,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFB KD,U2AF2B KD,U2AF2B knockdown,,treatment:U2AF2B morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF2B KD,U2AFB KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_5_1.fastq.gz zebrafish_U2af2KD_5_2.fastq.gz,fastq fastq,3657236866.0,18105133.0,u2af2b kd,0:101 1:101,A:859906359;C:963846892;G:950183263;T:882292781;N:1007571,101,101,,,859906359,963846892,950183263,882292781,1007571,SRX1092139,SRS987762,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.87685,0.87325,0.21282,0.21347,0.74899,0.75166,0.65013,0.65163,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39753,SRR2422941,SRX1092136,SRS987760,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,Control1,Control1,Control1,,treatment:Control 1|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 1,Control1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_1_2.fastq.gz zebrafish_U2af2KD_1_1.fastq.gz,fastq fastq,5446154724.0,26961162.0,control1,0:101 1:101,A:1236792250;C:1484635192;G:1463483173;T:1259686822;N:1557287,101,101,,,1236792250,1484635192,1463483173,1259686822,1557287,SRX1092136,SRS987760,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.88645,0.88416,0.23061,0.23167,0.75872,0.75921,0.63459,0.63891,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39754,SRR2422967,SRX1092138,SRS987763,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,U2AFA KD,U2AF2A KD,U2AF2A knockdown,,treatment:U2AF2A morpholino|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,U2AF A KD,U2AFA KD,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_4_1.fastq.gz zebrafish_U2af2KD_4_2.fastq.gz,fastq fastq,7385905174.0,36563887.0,u2af2a kd,0:101 1:101,A:1742999157;C:1956220866;G:1920103000;T:1764198542;N:2383609,101,101,,,1742999157,1956220866,1920103000,1764198542,2383609,SRX1092138,SRS987763,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.74404,0.74051,0.14971,0.14762,0.76641,0.76757,0.56197,0.56515,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39755,SRR2422942,SRX1092137,SRS987761,SRP060685,PRJNA289590,Danio rerio Raw sequence reads,PRJNA289590,Whole Genome Sequencing,The Goal of the study is to compare RNA expression especially splicing profiles in wildtype and U2af2 KD zebrafish,,,Control2,Control2,Control2,,treatment:Control 2|developmental stage:embryo|age:24 hours|strain:wildtype|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal,,,,,,,,,control 2,Control 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2000,2020Application ReadForward11Application ReadReverse102,SRP060685,,,zebrafish_U2af2KD_3_1.fastq.gz zebrafish_U2af2KD_3_2.fastq.gz,fastq fastq,4226478926.0,20923163.0,control2,0:101 1:101,A:1005765442;C:1098720686;G:1084955814;T:1035764094;N:1272890,101,101,,,1005765442,1098720686,1084955814,1035764094,1272890,SRX1092137,SRS987761,SRA276795,Brown University|Fairbrother Lab,Brown University,2,0.83225,0.83092,0.22325,0.22374,0.75396,0.75603,0.6203,0.61868,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-19,Pharyngula,Embryo,Whole Organism,All anatomical structures
39934,SRR2473238,SRX1270438,SRS1078341,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio embryos ectopically expressing human SPOPwt.,,Danio rerio ectopic SPOPwt,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOPwt,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOPwt,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,WT_CAGATC_L001_R1.fastq.gz WT_CAGATC_L001_R2.fastq.gz,fastq fastq,6185345892.0,60640646.0,Danio rerio ectopic SPOPwt,0:51 1:51,A:1647678166;C:1462773970;G:1416249443;T:1657464504;N:1179809,51,51,,,1647678166,1462773970,1416249443,1657464504,1179809,SRX1270438,SRS1078341,,,Weill Cornell Medical College,2,0.94598,0.94553,0.09216,0.0934,0.68789,0.69065,0.46814,0.47172,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
39935,SRR2473236,SRX1270437,SRS1078340,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,Danio rerio ectopically expressing SPOP F133V,,Danio rerio ectopic SPOP F133V,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,SPOP mutation leads to genomic instability in prostate cancer,Danio rerio ectopic SPOP F133V,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio ectopic SPOP F133V,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,Mut_GATCAG_L001_R2.fastq.gz Mut_GATCAG_L001_R1.fastq.gz,fastq fastq,6130528134.0,60103217.0,Danio rerio ectopic SPOP F133V,0:51 1:51,A:1630145057;C:1450811256;G:1409924927;T:1638457859;N:1189035,51,51,,,1630145057,1450811256,1409924927,1638457859,1189035,SRX1270437,SRS1078340,,,Weill Cornell Medical College,2,0.9444,0.94139,0.09809,0.0979,0.68487,0.68657,0.46751,0.47276,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2015-09-21,Pharyngula,Embryo,Whole Organism,All anatomical structures
39936,SRR2473235,SRX1270436,SRS1078339,SRP063952,PRJNA296414,SPOP mutation leads to genomic instability in prostate cancer,PRJNA296414,Transcriptome Analysis,Examination of the effects of morpholino based SPOP knockdown or ectopic expression of prostate cancer specific SPOP mutant F133V on the transcriptome of zebrafish embryos.,,,,,Danio rerio SPOP morpholino,,strain:AB/T|age:24 HPF|sex:pooled male and female|tissue:whole embryo|biomaterial provider:Yariv Houvras|BioSampleModel:Model organism or animal,,,,,,,,,Danio rerio SPOP morpholino,Danio rerio SPOP morpholino,1,SPOP mutation leads to genomic instability in prostate cancer RNA seq: Danio rerio SPOP morpholino,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1020Application ReadForward11Application ReadReverse52,SRP063952,,,Mock_ACTTGA_L001_R1.fastq.gz Mock_ACTTGA_L001_R2.fastq.gz,fastq fastq,5693947938.0,55823019.0,Danio rerio SPOP morpholino,0:51 1:51,A:1513477521;C:1350461483;G:1305374194;T:1523527099;N:1107641,51,51,,,1513477521,1350461483,1305374194,1523527099,1107641,SRX1270436,SRS1078339,,,Weill Cornell Medical College,2,0.94534,0.94431,0.09368,0.0945,0.68941,0.69077,0.46543,0.46749,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,United States,2016-02-17,Pharyngula,Embryo,Whole Organism,All anatomical structures
40711,SRR3420419,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00719_SEQ0107_R1.fastq.gz AG00719_SEQ0107_R2.fastq.gz,fastq fastq,2419781176.0,15919613.0,AG00719 run 1,0:76 1:76,A:738997601;C:465047900;G:477140497;T:733241052;N:5354126,76,76,,,738997601,465047900,477140497,733241052,5354126,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.78184,0.71182,0.66469,0.60037,0.75743,0.77518,0.53432,0.52801,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40712,SRR3420420,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00719_SEQ0181_R2.fastq.gz AG00719_SEQ0181_R1.fastq.gz,fastq fastq,3074724552.0,20228451.0,AG00719 run 2,0:76 1:76,A:918671897;C:609510609;G:622542852;T:922439528;N:1559666,76,76,,,918671897,609510609,622542852,922439528,1559666,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76444,0.65488,0.65157,0.55185,0.75741,0.78106,0.53067,0.52622,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40713,SRR3420421,SRX1660357,SRS1360318,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00719 8h 2,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00719 8h 2,AG00719 8h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00719_SEQ0288_R1.fastq.gz AG00719_SEQ0288_R2.fastq.gz,fastq fastq,2666395856.0,17542078.0,AG00719 run 3,0:76 1:76,A:787508876;C:539791618;G:549145516;T:785088342;N:4861504,76,76,,,787508876,539791618,549145516,785088342,4861504,SRX1660357,SRS1360318,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.75479,0.69465,0.63843,0.58422,0.75716,0.78423,0.53952,0.52615,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40714,SRR3420388,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00718_SEQ0107_R2.fastq.gz AG00718_SEQ0107_R1.fastq.gz,fastq fastq,2699903800.0,17762525.0,AG00718 run 1,0:76 1:76,A:832300161;C:503956886;G:525141498;T:832566681;N:5938574,76,76,,,832300161,503956886,525141498,832566681,5938574,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76651,0.69033,0.63937,0.56749,0.77145,0.78545,0.53429,0.53165,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40715,SRR3420392,SRX1660356,SRS1360315,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00718 8h 1,,strain:TUAB|age:8h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00718 8h 1,AG00718 8h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00718_SEQ0183_R2.fastq.gz AG00718_SEQ0183_R1.fastq.gz,fastq fastq,2798947456.0,18414128.0,AG00718 run 2,0:76 1:76,A:853546590;C:536347349;G:556751964;T:851863324;N:438229,76,76,,,853546590,536347349,556751964,851863324,438229,SRX1660356,SRS1360315,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74665,0.63683,0.6265,0.5237,0.76134,0.7905,0.54613,0.53982,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40716,SRR3420398,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00717_SEQ0107_R1.fastq.gz AG00717_SEQ0107_R2.fastq.gz,fastq fastq,1442918520.0,9492885.0,AG00717 run 1,0:76 1:76,A:442675510;C:273265985;G:284514997;T:439403136;N:3058892,76,76,,,442675510,273265985,284514997,439403136,3058892,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.76736,0.69048,0.60693,0.53532,0.74647,0.76138,0.51546,0.5135,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40717,SRR3420402,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00717_SEQ0179_R1.fastq.gz AG00717_SEQ0179_R2.fastq.gz,fastq fastq,2524099688.0,16605919.0,AG00717 run 2,0:76 1:76,A:752163917;C:500880325;G:526291920;T:744462824;N:300702,76,76,,,752163917,500880325,526291920,744462824,300702,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.7274,0.651,0.57791,0.50498,0.74434,0.76329,0.51831,0.50479,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40718,SRR3420405,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00717_SEQ0287_R1.fastq.gz AG00717_SEQ0287_R2.fastq.gz,fastq fastq,1320586032.0,8688066.0,AG00717 run 3,0:76 1:76,A:394339370;C:259687848;G:270914284;T:389960707;N:5683823,76,76,,,394339370,259687848,270914284,389960707,5683823,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72219,0.6734,0.55665,0.5122,0.75371,0.76323,0.5098,0.50658,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40719,SRR3420409,SRX1660355,SRS1360316,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00717 6h 2,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CTTGTA|BioSampleModel:Model organism or animal,,,,,,,,,AG00717 6h 2,AG00717 6h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00717_SEQ0299_R1.fastq.gz AG00717_SEQ0299_R2.fastq.gz,fastq fastq,1778143272.0,11698311.0,AG00717 run 4,0:76 1:76,A:531893644;C:351009327;G:366187476;T:528937189;N:115636,76,76,,,531893644,351009327,366187476,528937189,115636,SRX1660355,SRS1360316,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.72027,0.6573,0.57252,0.50814,0.74913,0.77479,0.51537,0.50066,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40720,SRR3420315,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00716_SEQ0107_R2.fastq.gz AG00716_SEQ0107_R1.fastq.gz,fastq fastq,1837024424.0,12085687.0,AG00716 run 1,0:76 1:76,A:571581150;C:339887376;G:357200726;T:564453542;N:3901630,76,76,,,571581150,339887376,357200726,564453542,3901630,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.77818,0.69777,0.64211,0.56481,0.75503,0.76926,0.50584,0.51507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40721,SRR3420319,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00716_SEQ0179_R2.fastq.gz AG00716_SEQ0179_R1.fastq.gz,fastq fastq,2763994600.0,18184175.0,AG00716 run 2,0:76 1:76,A:841712204;C:530711238;G:562110067;T:828853061;N:608030,76,76,,,841712204,530711238,562110067,828853061,608030,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74716,0.66787,0.61425,0.53764,0.7475,0.76518,0.50855,0.51311,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40722,SRR3420323,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00716_SEQ0287_R1.fastq.gz AG00716_SEQ0287_R2.fastq.gz,fastq fastq,1055704904.0,6945427.0,AG00716 run 3,0:76 1:76,A:323142351;C:199674907;G:210508599;T:317806564;N:4572483,76,76,,,323142351,199674907,210508599,317806564,4572483,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.73664,0.68701,0.59387,0.5447,0.76179,0.76132,0.51299,0.51552,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Gastrula,Embryo,Whole Organism,All anatomical structures
40723,SRR3420327,SRX1660354,SRS1360300,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00716 6h 1,,strain:TUAB|age:6h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GATCAG|BioSampleModel:Model organism or animal,,,,,,,,,AG00716 6h 1,AG00716 6h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00716_SEQ0296_R2.fastq.gz AG00716_SEQ0296_R1.fastq.gz,fastq fastq,2526928408.0,16624529.0,AG00716 run 4,0:76 1:76,A:771333886;C:482964782;G:508687112;T:763609426;N:333202,76,76,,,771333886,482964782,508687112,763609426,333202,SRX1660354,SRS1360300,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.74535,0.66478,0.61452,0.53584,0.75826,0.77329,0.51139,0.51539,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-04-22,Gastrula,Embryo,Whole Organism,All anatomical structures
40724,SRR3420333,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00715_SEQ0107_R1.fastq.gz AG00715_SEQ0107_R2.fastq.gz,fastq fastq,2314408088.0,15226369.0,AG00715 run 1,0:76 1:76,A:652783335;C:485705748;G:507451689;T:663544778;N:4922538,76,76,,,652783335,485705748,507451689,663544778,4922538,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59859,0.55293,0.24175,0.21943,0.78384,0.79174,0.52173,0.52111,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40725,SRR3420337,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00715_SEQ0179_R1.fastq.gz AG00715_SEQ0179_R2.fastq.gz,fastq fastq,2461668424.0,16195187.0,AG00715 run 2,0:76 1:76,A:653884256;C:562168304;G:597853484;T:647470498;N:291882,76,76,,,653884256,562168304,597853484,647470498,291882,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.5374,0.51402,0.2167,0.19427,0.78575,0.7934,0.52714,0.53043,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40726,SRR3420341,SRX1660350,SRS1360304,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00715 4h 2,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CAGATC|BioSampleModel:Model organism or animal,,,,,,,,,AG00715 4h 2,AG00715 4h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00715_SEQ0287_R1.fastq.gz AG00715_SEQ0287_R2.fastq.gz,fastq fastq,3692351624.0,24291787.0,AG00715 run 3,0:76 1:76,A:984283909;C:835828915;G:881112020;T:975490829;N:15635951,76,76,,,984283909,835828915,881112020,975490829,15635951,SRX1660350,SRS1360304,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.54752,0.52404,0.18037,0.16908,0.79358,0.7961,0.50982,0.50975,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40727,SRR3420346,SRX1660346,SRS1360308,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00714_SEQ0107_R1.fastq.gz AG00714_SEQ0107_R2.fastq.gz,fastq fastq,2377192296.0,15639423.0,AG00714 run 1,0:76 1:76,A:694380135;C:473427723;G:496920379;T:707435115;N:5028944,76,76,,,694380135,473427723,496920379,707435115,5028944,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.69444,0.63521,0.40011,0.36148,0.76252,0.77116,0.50751,0.5108,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40728,SRR3420349,SRX1660346,SRS1360308,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00714 4h 1,,strain:TUAB|age:4h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:GCCAAT|BioSampleModel:Model organism or animal,,,,,,,,,AG00714 4h 1,AG00714 4h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00714_SEQ0287_R1.fastq.gz AG00714_SEQ0287_R2.fastq.gz,fastq fastq,1841902256.0,12117778.0,AG00714 run 2,0:76 1:76,A:517451432;C:392444197;G:415696773;T:508506741;N:7803113,76,76,,,517451432,392444197,415696773,508506741,7803113,SRX1660346,SRS1360308,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63625,0.60304,0.3341,0.31189,0.77224,0.77703,0.50754,0.51039,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40729,SRR3420359,SRX1660342,SRS1360312,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00713_SEQ0107_R1.fastq.gz AG00713_SEQ0107_R2.fastq.gz,fastq fastq,2674764976.0,17597138.0,AG00713 run 1,0:76 1:76,A:738399424;C:560443522;G:578733188;T:791450319;N:5738523,76,76,,,738399424,560443522,578733188,791450319,5738523,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.63595,0.60509,0.17579,0.17695,0.79066,0.79815,0.49657,0.4916,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40730,SRR3420362,SRX1660342,SRS1360312,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00713 3h 2,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ACAGTG|BioSampleModel:Model organism or animal,,,,,,,,,AG00713 3h 2,AG00713 3h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00713_SEQ0287_R1.fastq.gz AG00713_SEQ0287_R2.fastq.gz,fastq fastq,2463895376.0,16209838.0,AG00713 run 2,0:76 1:76,A:661360403;C:556078326;G:581335469;T:654625128;N:10496050,76,76,,,661360403,556078326,581335469,654625128,10496050,SRX1660342,SRS1360312,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.58767,0.56878,0.14864,0.14485,0.79476,0.79898,0.49508,0.49769,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40731,SRR3420369,SRX1660341,SRS1360313,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00712_SEQ0107_R2.fastq.gz AG00712_SEQ0107_R1.fastq.gz,fastq fastq,1354427464.0,8910707.0,AG00712 run 1,0:76 1:76,A:382647488;C:281900295;G:291990859;T:395032379;N:2856443,76,76,,,382647488,281900295,291990859,395032379,2856443,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.64156,0.60052,0.23835,0.22296,0.78025,0.78717,0.49813,0.49898,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40732,SRR3420375,SRX1660341,SRS1360313,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00712 3h 1,,strain:TUAB|age:3h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:TGACCA|BioSampleModel:Model organism or animal,,,,,,,,,AG00712 3h 1,AG00712 3h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00712_SEQ0183_R1.fastq.gz AG00712_SEQ0183_R2.fastq.gz,fastq fastq,2335782480.0,15366990.0,AG00712 run 2,0:76 1:76,A:638971995;C:517112038;G:538588809;T:640731763;N:377875,76,76,,,638971995,517112038,538588809,640731763,377875,SRX1660341,SRS1360313,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60525,0.56571,0.24772,0.21069,0.77043,0.78543,0.50862,0.50386,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40733,SRR3420379,SRX1660340,SRS1360314,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00711_SEQ0107_R1.fastq.gz AG00711_SEQ0107_R2.fastq.gz,fastq fastq,2343343264.0,15416732.0,AG00711 run 1,0:76 1:76,A:645206414;C:505367235;G:523792864;T:663977432;N:4999319,76,76,,,645206414,505367235,523792864,663977432,4999319,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.59395,0.56211,0.10259,0.10243,0.80598,0.80911,0.51352,0.53772,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40734,SRR3420383,SRX1660340,SRS1360314,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00711 2.5h 2,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:CGATGT|BioSampleModel:Model organism or animal,,,,,,,,,AG00711 2.5h 2,AG00711 2.5h 2,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00711_SEQ0287_R1.fastq.gz AG00711_SEQ0287_R2.fastq.gz,fastq fastq,2668460776.0,17555663.0,AG00711 run 2,0:76 1:76,A:709820753;C:602900273;G:626554840;T:717828006;N:11356904,76,76,,,709820753,602900273,626554840,717828006,11356904,SRX1660340,SRS1360314,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.56281,0.54232,0.09217,0.09047,0.80657,0.81018,0.50757,0.52507,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40735,SRR3420304,SRX1660339,SRS1360299,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00710_SEQ0107_R1.fastq.gz AG00710_SEQ0107_R2.fastq.gz,fastq fastq,2705199784.0,17797367.0,AG00710 run 1,0:76 1:76,A:737065338;C:573787464;G:595216660;T:793361986;N:5768336,76,76,,,737065338,573787464,595216660,793361986,5768336,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.60426,0.58122,0.08196,0.09224,0.80578,0.8075,0.50121,0.50121,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,Whole Organism,All anatomical structures
40736,SRR3420308,SRX1660339,SRS1360299,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish Xenopus mouse and Drosophila and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus the ribosome interprets two codes within the mRNA the genetic code which specifies the amino acid sequence and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG00710 2.5h 1,,strain:TUAB|age:2.5h|sex:pooled male and female|tissue:whole embryo|treatment:alpha amanitin|barcode:ATCACG|BioSampleModel:Model organism or animal,,,,,,,,,AG00710 2.5h 1,AG00710 2.5h 1,1,1,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,PAIRED,ILLUMINA,Illumina HiSeq 2500,1500Application ReadForward11Application ReadReverse76,SRP072296,,,AG00710_SEQ0287_R1.fastq.gz AG00710_SEQ0287_R2.fastq.gz,fastq fastq,2275540168.0,14970659.0,AG00710 run 2,0:76 1:76,A:614429428;C:505827101;G:528906356;T:616697803;N:9679480,76,76,,,614429428,505827101,528906356,616697803,9679480,SRX1660339,SRS1360299,SRA395141,Yale University|Giraldez Lab,Yale University,2,0.57792,0.56382,0.07268,0.07246,0.80261,0.80612,0.49743,0.50296,76,76,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Blastula,Embryo,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.,,,sample04,,dkc1 elu1 mut1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,562954867,599474858,575980257,687194946,134250,SRX6047142,SRS4950160,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.96592,,0.05193,,0.69181,,0.46287,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,sample03,,dkc1 elu1 sib3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,617606365,576906982,574368411,756144418,135770,SRX6047141,SRS4950159,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95481,,0.09246,,0.70187,,0.48651,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,sample02,,dkc1 elu1 sib2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,594107753,588927623,585955773,731305179,457261,SRX6047140,SRS4950158,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95785,,0.07623,,0.70512,,0.49187,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,sample01,,dkc1 elu1 sib1,,isolate:biological replicate 1|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:wild|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,594796815,658132193,620365621,738201586,146935,SRX6047139,SRS4950157,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.97084,,0.05106,,0.69858,,0.46901,,73,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,sample06,,dkc1 elu1 mut3,,isolate:biological replicate 3|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,603400760,568138093,589455352,742564020,225074,SRX6047138,SRS4950156,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95328,,0.08246,,0.69581,,0.48805,,74,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,sample05,,dkc1 elu1 mut2,,isolate:biological replicate 2|breed:elu1|dev stage:larval|sex:not determined|tissue:whole organism|phenotype:mutant|BioSampleModel:Model organism or animal,,,,,,,,,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.,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP201168,,,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,,,590961375,565727869,562583560,718173630,254777,SRX6047137,SRS4950155,SRA897402,Eotvos Lorand University|Genetics,Eotvos Lorand University,1,0.95589,,0.07601,,0.70317,,0.49704,,75,,B,,usable mapping rate,illumina,nextseq,unknown,unknown,unknown,bulk,unknown,unknown,,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.,,,,,5b,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5b,5b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,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,,,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,,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.,,,,,5a,,strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,5a,5a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,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,,,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,,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.,,,,,2b,,strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,2b,2b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,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,,,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,,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.,,,,,2a,,strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,2a,2a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,NextSeq 500,,SRP221273,,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,,,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,,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.,,,,,1b,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1b,1b,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,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,,,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,,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. 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.,,,,,1a,,strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1a|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of whole zebrafish embryos,1a,1a,10X v2 chromium cDNA library,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP221273,,loader:latf load,olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq,fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq,99552249225.0,626114775.0,1a.gz,0:26 1:133,A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522,26,133,,,27540748865,22111148705,23108024457,26777444676,14882522,SRX6828140,SRS5370315,SRA960102,University of Oregon|Institute of Neuroscience,University of Oregon,2,0.01166,0.95413,0.002,0.08635,0.9779,0.80034,0.44044,0.48046,26,133,T,B,sc-like readlen,illumina,hiseq_era,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United States,2019-12-10,Pharyngula,Embryo,Whole Organism,All anatomical structures
74579,SRR23974542,SRX19779002,SRS17142416,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D1,,isolate:10|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,10,10,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP1F.fq.gz,fastq,2956240050.0,19708267.0,TP1F.fq.gz,0:150 1:0,A:785689496;C:695356949;G:702558232;T:772610474;N:24899,150,0,,,785689496,695356949,702558232,772610474,24899,SRX19779002,SRS17142416,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93915,,0.07675,,0.68534,,0.4891,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74580,SRR23974543,SRX19779001,SRS17142414,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C3,,isolate:9|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,9,9,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP3F.fq.gz,fastq,3243688800.0,21624592.0,CP3F.fq.gz,0:150 1:0,A:866441929;C:744536766;G:783433493;T:849247758;N:28854,150,0,,,866441929,744536766,783433493,849247758,28854,SRX19779001,SRS17142414,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.91011,,0.086,,0.68972,,0.48291,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74581,SRR23974544,SRX19779000,SRS17142415,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C2,,isolate:8|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,8,8,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP2F.fq.gz,fastq,3455536800.0,23036912.0,CP2F.fq.gz,0:150 1:0,A:955162327;C:765147222;G:797594182;T:937601078;N:31991,150,0,,,955162327,765147222,797594182,937601078,31991,SRX19779000,SRS17142415,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90361,,0.13207,,0.69345,,0.48842,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74582,SRR23974545,SRX19778999,SRS17142412,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,C1,,isolate:7|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae parental,7,7,control larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CP1F.fq.gz,fastq,3394157850.0,22627719.0,CP1F.fq.gz,0:150 1:0,A:918865518;C:780289302;G:793602009;T:901371269;N:29752,150,0,,,918865518,780289302,793602009,901371269,29752,SRX19778999,SRS17142412,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93417,,0.08314,,0.68006,,0.48695,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74583,SRR23974546,SRX19778998,SRS17142413,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B3,,isolate:6|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,6,6,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE3F.fq.gz,fastq,3021012750.0,20140085.0,TE3F.fq.gz,0:150 1:0,A:802754479;C:697084034;G:736507600;T:784641365;N:25272,150,0,,,802754479,697084034,736507600,784641365,25272,SRX19778998,SRS17142413,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.9039,,0.08388,,0.6997,,0.49603,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74584,SRR23974547,SRX19778997,SRS17142411,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B2,,isolate:5|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,5,5,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE2F.fq.gz,fastq,3037657950.0,20251053.0,TE2F.fq.gz,0:150 1:0,A:806162990;C:709397050;G:731668622;T:790403768;N:25520,150,0,,,806162990,709397050,731668622,790403768,25520,SRX19778997,SRS17142411,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.92641,,0.07865,,0.69798,,0.46929,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74585,SRR23974548,SRX19778996,SRS17142410,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed larvae,B1,,isolate:4|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Gly larvae exposed,4,4,larvae exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TE1F.fq.gz,fastq,3459122100.0,23060814.0,TE1F.fq.gz,0:150 1:0,A:957107791;C:768667835;G:795319703;T:937996052;N:30719,150,0,,,957107791,768667835,795319703,937996052,30719,SRX19778996,SRS17142410,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.90435,,0.12237,,0.70128,,0.47725,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74586,SRR23974549,SRX19778995,SRS17142409,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A3,,isolate:3|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,3,3,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE3F.fq.gz,fastq,3496645950.0,23310973.0,CE3F.fq.gz,0:150 1:0,A:927418130;C:820945235;G:834908249;T:913344868;N:29468,150,0,,,927418130,820945235,834908249,913344868,29468,SRX19778995,SRS17142409,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.93227,,0.08275,,0.69339,,0.49066,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74587,SRR23974550,SRX19778994,SRS17142408,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D3,,isolate:12|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:3|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,12,12,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP3F.fq.gz,fastq,3317790150.0,22118601.0,TP3F.fq.gz,0:150 1:0,A:883540292;C:768555339;G:796741351;T:868924072;N:29096,150,0,,,883540292,768555339,796741351,868924072,29096,SRX19778994,SRS17142408,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74588,SRR23974551,SRX19778993,SRS17142407,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,exposed parents,D2,,isolate:11|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:1000|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Gly parental larvae,11,11,larvae of parents exposed to glyphosate,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,TP2F.fq.gz,fastq,2948738400.0,19658256.0,TP2F.fq.gz,0:150 1:0,A:777218056;C:697066948;G:709846212;T:764582431;N:24753,150,0,,,777218056,697066948,709846212,764582431,24753,SRX19778993,SRS17142407,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74589,SRR23974552,SRX19778992,SRS17142405,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A2,,isolate:2|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:2|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,2,2,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE2F.fq.gz,fastq,3760293450.0,25068623.0,CE2F.fq.gz,0:150 1:0,A:1000790271;C:868241486;G:905025923;T:986203921;N:31849,150,0,,,1000790271,868241486,905025923,986203921,31849,SRX19778992,SRS17142405,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures
74590,SRR23974553,SRX19778991,SRS17142406,SRP429402,PRJNA944264,Danio rerio Raw sequence reads,PRJNA944264,Other,17 dpf larvae exposed to glyphosate and parents exposed to glyphosate,,,,Control,A1,,isolate:1|age:17 dpf|sex:not applicable|tissue:complete larva|sample type:Pool|treatment:0|replicate:1|BioSampleModel:Model organism or animal,,,,,,,,,Control larvae,1,1,larvae control,,,RNA-Seq,TRANSCRIPTOMIC,unspecified,SINGLE,ILLUMINA,Illumina HiSeq 1500,,SRP429402,,,CE1F.fq.gz,fastq,3446794950.0,22978633.0,CE1F.fq.gz,0:150 1:0,A:916043654;C:787898255;G:842788936;T:900033406;N:30699,150,0,,,916043654,787898255,842788936,900033406,30699,SRX19778991,SRS17142406,SRA1610960,Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology,Centro de Investigacion en Alimentacion y Desarrollo,1,0.89022,,0.09813,,0.69954,,0.49171,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,unknown,unknown,bulk,unknown,unknown,,Mexico,2023-03-27,Larval,Larval,Whole Organism,All anatomical structures