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171 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "unspecified" and experiment.library_strategy = "RNA-Seq"

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devstage_curation 10

tissue_curation 6

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technology 3

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  • RNA-Seq · 171 ✖

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experiment.library_layout 1

  • SINGLE · 171 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
10056 10056 ERR4691987 ERX4613068 ERS5216074 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457891 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_2.fastq.gz fastq 1291626898.0 35072619.0 ena RUN UCLA 16 10 2020 22:30:43:819 4 0:36.83 1:0 A:364596432;C:305716590;G:295397140;T:324498501;N:1418235 36 0     364596432 305716590 295397140 324498501 1418235 ERX4613068 ERS5216074 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.93311   0.08182   0.75852   0.54813   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10057 10057 ERR4691986 ERX4613067 ERS5216073 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457890 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 MCU_1.fastq.gz fastq 1236033124.0 33559740.0 ena RUN UCLA 16 10 2020 22:30:43:819 3 0:36.83 1:0 A:348518065;C:293502111;G:279181983;T:313506799;N:1324166 36 0     348518065 293502111 279181983 313506799 1324166 ERX4613067 ERS5216073 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92798   0.07907   0.7697   0.5488   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10058 10058 ERR4691985 ERX4613066 ERS5216072 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457889 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_2.fastq.gz fastq 1180831209.0 32069533.0 ena RUN UCLA 16 10 2020 22:30:43:819 2 0:36.82 1:0 A:328604642;C:281065336;G:278743466;T:291039015;N:1378750 36 0     328604642 281065336 278743466 291039015 1378750 ERX4613066 ERS5216072 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92319   0.08946   0.75706   0.49996   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
10059 10059 ERR4691984 ERX4613065 ERS5216071 ERP124560 PRJEB40865 RNA seq of zebrafish adult MCU mutant hearts ena-STUDY-UCLA-16-10-2020-22:30:44:295-390 Other We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity but exhibits cardiac function and structure defects. We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart. ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16     zebrafish adult heart RNA SAMEA7457888 UCLA ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart                 Illumina HiSeq 3000 sequencing ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 3000   ERP124560 Illumina HiSeq 3000 sequencing ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21 WT_1.fastq.gz fastq 1428414407.0 38793098.0 ena RUN UCLA 16 10 2020 22:30:43:819 1 0:36.82 1:0 A:398925739;C:338731211;G:333527196;T:355553981;N:1676280 36 0     398925739 338731211 333527196 355553981 1676280 ERX4613065 ERS5216071 ERA2987364 European Nucleotide Archive University of California, Los Angeles, USA 1 0.92407   0.08758   0.75726   0.4969   37   B   usable mapping rate illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2020-10-16 Adult Adult Heart Cardiovascular System
36581 36581 SRR594769 SRX195432 SRS369361 SRP016134 PRJNA177654 Danio rerio Transcriptome or Gene expression PRJNA177654 Other We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.     1 Test GFP Negative 1                     Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development Embryos 1 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP016134         2525199228.0 65962848.0 GFP Positive 0:38.28 A:665802914;C:594493287;G:612298433;T:652078696;N:525898 38       665802914 594493287 612298433 652078696 525898 SRX195432 SRS369361     University of Cambridge 1 0.89062   0.09595   0.74059   0.47506   36   B   usable mapping rate illumina early_illumina unknown unknown unknown bulk unknown unknown   United Kingdom 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
36582 36582 SRR594771 SRX195432 SRS369361 SRP016134 PRJNA177654 Danio rerio Transcriptome or Gene expression PRJNA177654 Other We use zebrafish embryos to characterise the transcriptome of the developing blood and endothelium.     1 Test GFP Negative 1                     Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development Embryos 1 1     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>40</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP016134     gfp_negative_replicate_1_sequence.txt.gz fastq 2549682148.0 66546682.0 GFP Negative 0:38.31 A:686329592;C:587342682;G:601330559;T:674194074;N:485241 38       686329592 587342682 601330559 674194074 485241 SRX195432 SRS369361     University of Cambridge 1 0.90413   0.13272   0.71342   0.48186   36   B   usable mapping rate illumina early_illumina unknown unknown unknown bulk unknown unknown   United Kingdom 2015-07-22 Undetermined Embryo Embryo Imprecise All anatomical structures
36739 36739 SRR867022 SRX286270 SRS420566 SRP022549 PRJNA202401 Danio rerio Transcriptome or Gene expression PRJNA202401 Other Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.     Full transcriptome analysis of early dorsoventral DV patterning in zebrafish General Sample for Danio rerio ICH   strain:wild type                 Full transcriptome analysis of early dorsoventral DV patterning in zebrafish Bcat Danio rerio boot 1 RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ABI_SOLID AB SOLiD 3 Plus System <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP022549     s0205_20091123_4_Boot2_F3_QV.qual s0205_20091123_4_Boot2_F3.csfasta SOLiD_native SOLiD_native 9801985250.0 196039705.0 Zebrafish DV patterning Boot 0:50 0:2587797600;1:2275478534;2:2625317272;3:2293877905;.:19513939 50                 SRX286270 SRS420566 SRA075737 BAYGEN|NGSP BAYGEN 1 0.59289   0.09435   0.92669   0.7658   50   B   usable mapping rate legacy early 3prime rrna_depletion unknown bulk unknown unknown   Hungary 2013-05-23 Undetermined Undetermined Undetermined Undetermined
36740 36740 SRR867023 SRX286271 SRS420566 SRP022549 PRJNA202401 Danio rerio Transcriptome or Gene expression PRJNA202401 Other Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.     Full transcriptome analysis of early dorsoventral DV patterning in zebrafish General Sample for Danio rerio ICH   strain:wild type                 Full transcriptome analysis of early dorsoventral DV patterning in zebrafish ICH Danio rerio ICH 1 RNA quality and quantity measurements were performed on Bioanalyzer Agilent Technologies and Qubit Life Technologies. High quality RIN >8.5 total RNA samples from three biological replicates were pooled and processed using the SOLiD total RNA Seq Kit Life Technologies according to the manufacturers suggestions. Briefly 5mg of pooled RNA was DNaseI treated and the ribosomal RNA depleted using Eucaryote RiboMinues rRNA Removal Kit Life Technologies. The leftover was fragmented using RNaseIII the 50 200nt fraction size selected sequencing adaptors ligated and the templates reverse transcribed using ArrayScript RT. The cDNA library was purified with Qiagen MinElute PCR Purification Kit Qiagen and size selected on a 6% TBE Urea denaturing polyacrylamide gel. The 150 250nt cDNA fraction was amplified using AmpliTaq polymerase and purified by AmPureXP Beads Agencourt. Concentration of each library was determined using the SOLiD Library TaqMan Quantitation Kit Life Technologies. Each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR ePCR. Emulsions were broken with butanol and ePCR beads enriched for template positive beads by hybridization with magnetic enrichment beads. Template enriched beads were extended at the three prime end in the presence of terminal transferase and three prime bead linker. Beads with the clonally amplified DNA were deposited onto sequencing slide and sequenced on SOLiD V4 Instrument using the 50 base sequencing chemistry.     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ABI_SOLID AB SOLiD 3 Plus System <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP022549     s0205_20091123_4_ICH_F3.csfasta s0205_20091123_4_ICH_F3_QV.qual SOLiD_native SOLiD_native 10810535400.0 216210708.0 Zebrafish DV patterning ICH 0:50 0:2903579857;1:2528898611;2:2759865128;3:2553918387;.:64273417 50                 SRX286271 SRS420566 SRA075737 BAYGEN|NGSP BAYGEN 1 0.42474   0.06136   0.93434   0.75757   50   B   usable mapping rate legacy early 3prime rrna_depletion unknown bulk unknown unknown   Hungary 2013-05-23 Undetermined Undetermined Undetermined Undetermined
36761 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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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 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 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP059060     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
43099 43099 SRR5893058 SRX3058787 SRS2404528 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c PatA RPF input B2 mrna seq pata AG01431   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:2|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c PatA RPF input B2 AG01431.1 AG01431.1 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01431.1_R1.fastq.gz fastq 935580824.0 12310274.0 AG01431.1 R1.fastq.gz 0:76 A:188726598;C:276745094;G:258235229;T:211815415;N:58488 76       188726598 276745094 258235229 211815415 58488 SRX3058787 SRS2404528 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.89193   0.09644   0.7849   0.69832   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43100 43100 SRR5893059 SRX3058786 SRS2404528 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c PatA RPF input B2 mrna seq pata AG01431   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:2|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c PatA RPF input B2 AG01431.2 AG01431.2 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01431.2_R1.fastq.gz fastq 2550535528.0 33559678.0 AG01431.2 R1.fastq.gz 0:76 A:541016830;C:720948568;G:664552003;T:623742439;N:275688 76       541016830 720948568 664552003 623742439 275688 SRX3058786 SRS2404528 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.90466   0.10321   0.77595   0.60561   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43101 43101 SRR5893060 SRX3058785 SRS2404530 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c RPF input B1 mrna seq pata AG01432   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:r0|condition:input|replicate group:24|replicate:1|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c RPF input B1 AG01432.1 AG01432.1 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01432.1_R1.fastq.gz fastq 2796444700.0 36795325.0 AG01432.1 R1.fastq.gz 0:76 A:663756831;C:716464328;G:666812843;T:749363967;N:46731 76       663756831 716464328 666812843 749363967 46731 SRX3058785 SRS2404530 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.85828   0.09273   0.75534   0.50507   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43102 43102 SRR5893061 SRX3058784 SRS2404531 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c RPF input B2 mrna seq pata AG01433   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:r0|condition:input|replicate group:24|replicate:2|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c RPF input B2 AG01433.1 AG01433.1 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01433.1_R1.fastq.gz fastq 3208682532.0 42219507.0 AG01433.1 R1.fastq.gz 0:76 A:715292036;C:869176418;G:807214698;T:816945712;N:53668 76       715292036 869176418 807214698 816945712 53668 SRX3058784 SRS2404531 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.85439   0.09801   0.76597   0.58538   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43115 43115 SRR5893082 SRX3058763 SRS2404539 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c PatA RPF input B1 mrna seq pata AG01430   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:1|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c PatA RPF input B1 AG01430.2 AG01430.2 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01430.2_R1.fastq.gz fastq 3133028560.0 41224060.0 AG01430.2 R1.fastq.gz 0:76 A:672361176;C:875054552;G:808035984;T:777238497;N:338351 76       672361176 875054552 808035984 777238497 338351 SRX3058763 SRS2404539 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.88898   0.09238   0.77234   0.6234   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2018-06-07 Cleavage Embryo Embryo Imprecise All anatomical structures
43116 43116 SRR5893083 SRX3058762 SRS2404539 SRP114782 PRJNA397065 mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis PRJNA397065 Other RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.       mRNA Seq R0 patA WT 64c PatA RPF input B1 mrna seq pata AG01430   strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:PatA|molecule:RNA|selection:r0|condition:input|replicate group:23|replicate:1|BioSampleModel:Model organism or animal                 mRNA Seq R0 patA WT 64c PatA RPF input B1 AG01430.1 AG01430.1 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP114782     AG01430.1_R1.fastq.gz fastq 898114724.0 11817299.0 AG01430.1 R1.fastq.gz 0:76 A:187456862;C:260421633;G:242938837;T:207239930;N:57462 76       187456862 260421633 242938837 207239930 57462 SRX3058762 SRS2404539 SRA596275 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.87315   0.08685   0.78117   0.65305   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2017-08-03 Cleavage Embryo Embryo Imprecise All anatomical structures
51152 51152 SRR8552544 SRX5354346 SRS4345564 SRP184786 PRJNA521558 Brd4 and p300 confer transcriptional competency during zygotic genome activation PRJNA521558 Other The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.       mRNA seq WT 2h R0 mRNA seq WT 2h R0 AGN001827   strain:TU/AB|age:2.0|dev stage:64 cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS001459|replicate ref:AGN001827|replicate order:1|BioSampleModel:Model organism or animal                 mRNA seq WT 2h R0 AGR002489 AGR002489 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP184786     AGR002489_R1.fastq.gz fastq 1915424276.0 25202951.0 AGR002489 R1.fastq.gz 0:76 A:427998951;C:502027263;G:488957899;T:496384297;N:55866 76       427998951 502027263 488957899 496384297 55866 SRX5354346 SRS4345564 SRA847217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.83803   0.08509   0.75753   0.47975   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-02-08 Cleavage Embryo Embryo Imprecise All anatomical structures
51153 51153 SRR8552545 SRX5354345 SRS4345563 SRP184786 PRJNA521558 Brd4 and p300 confer transcriptional competency during zygotic genome activation PRJNA521558 Other The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.       mRNA seq 4h trip R0 mRNA seq 4h trip R0 AGN001745   strain:TU/AB|age:4.0|sex:pooled male and female|tissue:embryo|treatment:triptolide|molecule:RNA|selection:r0|sample ref:AGS001391|replicate ref:AGN001745|replicate order:1|BioSampleModel:Model organism or animal                 mRNA seq 4h trip R0 AGR002401 AGR002401 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP184786     AGR002401_R1.fastq.gz fastq 924494628.0 12164403.0 AGR002401 R1.fastq.gz 0:76 A:189288361;C:252171181;G:262503967;T:220509369;N:21750 76       189288361 252171181 262503967 220509369 21750 SRX5354345 SRS4345563 SRA847217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.69029   0.07606   0.77516   0.52854   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-06-12 Undetermined Embryo Embryo Imprecise All anatomical structures
51154 51154 SRR8552546 SRX5354344 SRS4345562 SRP184786 PRJNA521558 Brd4 and p300 confer transcriptional competency during zygotic genome activation PRJNA521558 Other The awakening of the genome post fertilization is a cornerstone of animal development. However the mechanisms that activate the silent genome post fertilization are poorly understood. Here we show that transcriptional competency in zebrafish is regulated by Brd4 and p300 dependent histone acetylation. Live imaging of transcription revealed that genome activation begins at the miR 430 locus is gradual and stochastic. We show that genome activation does not require slow down of the cell cycle and is regulated through translation of maternally inherited mRNAs. Among these the enhancer regulators p300 and Brd4 can prematurely activate transcription and restore transcriptional competency when maternal mRNA translation is blocked whereas inhibiting histone acetylation blocks genome activation. We conclude that p300 and Brd4 are sufficient to trigger genome wide transcriptional competency by regulating histone acetylation on the first zygotic genes in zebrafish. This mechanism is critical to initiating zygotic development and developmental reprogramming.       mRNA seq WT 4h R0 mRNA seq WT 4h R0 AGN001743   strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|condition:untreated|sample ref:AGS001389|replicate ref:AGN001743|replicate order:1|BioSampleModel:Model organism or animal                 mRNA seq WT 4h R0 AGR002398 AGR002398 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP184786     AGR002398_R1.fastq.gz fastq 1304401604.0 17163179.0 AGR002398 R1.fastq.gz 0:76 A:248973263;C:385894356;G:377042802;T:292460281;N:30902 76       248973263 385894356 377042802 292460281 30902 SRX5354344 SRS4345562 SRA847217 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.82485   0.15823   0.78847   0.75023   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2019-06-12 Blastula Embryo Embryo Imprecise All anatomical structures
52829 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 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 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 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 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 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 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 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 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 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 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 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
62489 62489 SRR13234605 SRX9666721 SRS7865658 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf triptolide ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 6h trip r0 AGN001795   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|treatment:triptolide|molecule:mRNA|selection:r0|sample ref:AGS001441|replicate ref:AGN001795|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf triptolide ribo0 AGR002455 AGR002455 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002455_R1.fastq.gz fastq 2342992220.0 30828845.0 AGR002455 R1.fastq.gz 0:76 1:0 A:486939172;C:667467813;G:688508751;T:499974142;N:102342 76 0     486939172 667467813 688508751 499974142 102342 SRX9666721 SRS7865658 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.49109   0.13387   0.79304   0.50899   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62490 62490 SRR13234606 SRX9666720 SRS7865657 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 6hpf shield polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 6h shield pA AGN000135   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |molecule:RNA|selection:pA|sample ref:AGS000123|replicate ref:AGN000135|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 6hpf shield polyA AGR000189 AGR000189 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000189_R1.fastq.gz fastq 3092161992.0 40686342.0 AGR000189 R1.fastq.gz 0:76 1:0 A:843616790;C:685315432;G:677129339;T:885937873;N:162558 76 0     843616790 685315432 677129339 885937873 162558 SRX9666720 SRS7865657 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93709   0.13352   0.75363   0.48096   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62491 62491 SRR13234607 SRX9666719 SRS7865656 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf untreated ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 6h r0 AGN001794   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:r0|sample ref:AGS001440|replicate ref:AGN001794|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf untreated ribo0 AGR002454 AGR002454 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002454_R1.fastq.gz fastq 2427554532.0 31941507.0 AGR002454 R1.fastq.gz 0:76 1:0 A:522620648;C:658233071;G:668206211;T:578388551;N:106051 76 0     522620648 658233071 668206211 578388551 106051 SRX9666719 SRS7865656 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.63583   0.17863   0.76861   0.50012   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62492 62492 SRR13234608 SRX9666718 SRS7865655 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf untreated ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 6h r0 AGN001793   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|molecule:mRNA|selection:r0|sample ref:AGS001439|replicate ref:AGN001793|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf untreated ribo0 AGR002453 AGR002453 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002453_R1.fastq.gz fastq 2027694820.0 26680195.0 AGR002453 R1.fastq.gz 0:76 1:0 A:419274134;C:549004017;G:566872772;T:492455226;N:88671 76 0     419274134 549004017 566872772 492455226 88671 SRX9666718 SRS7865655 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.61548   0.17157   0.76986   0.47549   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62493 62493 SRR13234609 SRX9666717 SRS7865654 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 4hpf untreated ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 4h r0 AGN001792   strain:TU/AB|age:4.0|dev stage:oblong sphere|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:r0|sample ref:AGS001438|replicate ref:AGN001792|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 4hpf untreated ribo0 AGR002452 AGR002452 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002452_R1.fastq.gz fastq 1904045784.0 25053234.0 AGR002452 R1.fastq.gz 0:76 1:0 A:367476235;C:535902395;G:555905669;T:444678465;N:83020 76 0     367476235 535902395 555905669 444678465 83020 SRX9666717 SRS7865654 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58727   0.11611   0.75306   0.49316   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Blastula Embryo Embryo Imprecise All anatomical structures
62494 62494 SRR13234610 SRX9666716 SRS7865653 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 4hpf untreated ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 4h r0 AGN001791   strain:TU/AB|age:4.0|dev stage:oblong sphere|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|molecule:mRNA|selection:r0|sample ref:AGS001437|replicate ref:AGN001791|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 4hpf untreated ribo0 AGR002451 AGR002451 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002451_R1.fastq.gz fastq 1573875944.0 20708894.0 AGR002451 R1.fastq.gz 0:76 1:0 A:321769770;C:430719516;G:442061050;T:379256409;N:69199 76 0     321769770 430719516 442061050 379256409 69199 SRX9666716 SRS7865653 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.62749   0.12425   0.75509   0.48966   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Blastula Embryo Embryo Imprecise All anatomical structures
62495 62495 SRR13234611 SRX9666715 SRS7865652 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf triptolide ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 2h trip r0 AGN001790   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |treatment:triptolide|molecule:mRNA|selection:r0|sample ref:AGS001436|replicate ref:AGN001790|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf triptolide ribo0 AGR002450 AGR002450 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002450_R1.fastq.gz fastq 2144910380.0 28222505.0 AGR002450 R1.fastq.gz 0:76 1:0 A:399114937;C:619699997;G:640831720;T:485170389;N:93337 76 0     399114937 619699997 640831720 485170389 93337 SRX9666715 SRS7865652 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.58138   0.05574   0.7655   0.5008   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Blastula Embryo Embryo Imprecise All anatomical structures
62496 62496 SRR13234612 SRX9666714 SRS7865651 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf untreated ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 2h r0 AGN001788   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:r0|sample ref:AGS001434|replicate ref:AGN001788|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf untreated ribo0 AGR002448 AGR002448 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002448_R1.fastq.gz fastq 2231107908.0 29356683.0 AGR002448 R1.fastq.gz 0:76 1:0 A:440870841;C:623696262;G:637307222;T:529136932;N:96651 76 0     440870841 623696262 637307222 529136932 96651 SRX9666714 SRS7865651 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.61872   0.05832   0.76242   0.49607   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Blastula Embryo Embryo Imprecise All anatomical structures
62497 62497 SRR13234613 SRX9666713 SRS7865650 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf untreated mRNA ribo0 MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 2h r0 AGN001787   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|molecule:mRNA|selection:r0|sample ref:AGS001433|replicate ref:AGN001787|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf untreated mRNA ribo0 AGR002447 AGR002447 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002447_R1.fastq.gz fastq 2042104116.0 26869791.0 AGR002447 R1.fastq.gz 0:76 1:0 A:403147476;C:577168316;G:592275766;T:469423534;N:89024 76 0     403147476 577168316 592275766 469423534 89024 SRX9666713 SRS7865650 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.63234   0.05374   0.77025   0.52125   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Blastula Embryo Embryo Imprecise All anatomical structures
62498 62498 SRR13234614 SRX9666712 SRS7865649 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf triptolide polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 6h trip pA AGN001786   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001432|replicate ref:AGN001786|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 6hpf triptolide polyA AGR002446 AGR002446 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002446_R1.fastq.gz fastq 1124283808.0 14793208.0 AGR002446 R1.fastq.gz 0:76 1:0 A:303085193;C:262065829;G:254422392;T:304661911;N:48483 76 0     303085193 262065829 254422392 304661911 48483 SRX9666712 SRS7865649 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.90758   0.10149   0.75298   0.50822   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62499 62499 SRR13234615 SRX9666711 SRS7865646 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf triptolide polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 6h trip pA AGN001785   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001431|replicate ref:AGN001785|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 6hpf triptolide polyA AGR002445 AGR002445 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002445_R1.fastq.gz fastq 982349780.0 12925655.0 AGR002445 R1.fastq.gz 0:76 1:0 A:263625214;C:224164362;G:222612457;T:271905809;N:41938 76 0     263625214 224164362 222612457 271905809 41938 SRX9666711 SRS7865646 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.90172   0.10357   0.75621   0.50493   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62500 62500 SRR13234616 SRX9666710 SRS7865648 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 4hpf untreated polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 4h pA AGN001782   strain:TU/AB|age:4.0|dev stage:oblong sphere|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:pA|sample ref:AGS001428|replicate ref:AGN001782|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 4hpf untreated polyA AGR002442 AGR002442 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002442_R1.fastq.gz fastq 1142796572.0 15036797.0 AGR002442 R1.fastq.gz 0:76 1:0 A:292287577;C:266816206;G:263293188;T:320349882;N:49719 76 0     292287577 266816206 263293188 320349882 49719 SRX9666710 SRS7865648 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92257   0.06557   0.74199   0.48749   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62501 62501 SRR13234617 SRX9666709 SRS7865647 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + U1U2 morpholino polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 6h shield U1U2 MO pA AGN000134   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:U1U2 morpholino|molecule:RNA|selection:pA|sample ref:AGS000122|replicate ref:AGN000134|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + U1U2 morpholino polyA AGR000188 AGR000188 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000188_R1.fastq.gz fastq 2315635336.0 30468886.0 AGR000188 R1.fastq.gz 0:76 1:0 A:650669894;C:502589633;G:490937822;T:670879962;N:558025 76 0     650669894 502589633 490937822 670879962 558025 SRX9666709 SRS7865647 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.91636   0.26406   0.78709   0.51247   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62502 62502 SRR13234618 SRX9666708 SRS7865645 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 4hpf untreated polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 4h pA AGN001781   strain:TU/AB|age:4.0|dev stage:oblong sphere|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|molecule:mRNA|selection:pA|sample ref:AGS001427|replicate ref:AGN001781|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 4hpf untreated polyA AGR002441 AGR002441 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002441_R1.fastq.gz fastq 1189818836.0 15655511.0 AGR002441 R1.fastq.gz 0:76 1:0 A:305378947;C:275869468;G:273664835;T:334853957;N:51629 76 0     305378947 275869468 273664835 334853957 51629 SRX9666708 SRS7865645 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92317   0.06463   0.74738   0.49227   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62503 62503 SRR13234619 SRX9666707 SRS7865644 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf triptolide polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 2h trip pA AGN001780   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001426|replicate ref:AGN001780|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf triptolide polyA AGR002440 AGR002440 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002440_R1.fastq.gz fastq 1112207104.0 14634304.0 AGR002440 R1.fastq.gz 0:76 1:0 A:312059705;C:265206647;G:242628256;T:292265252;N:47244 76 0     312059705 265206647 242628256 292265252 47244 SRX9666707 SRS7865644 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92073   0.03967   0.77431   0.48546   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62504 62504 SRR13234620 SRX9666706 SRS7865643 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf triptolide polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 2h trip pA AGN001779   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|treatment:triptolide|molecule:mRNA|selection:pA|sample ref:AGS001425|replicate ref:AGN001779|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf triptolide polyA AGR002439 AGR002439 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002439_R1.fastq.gz fastq 1105524500.0 14546375.0 AGR002439 R1.fastq.gz 0:76 1:0 A:281140999;C:255943600;G:257104944;T:311286892;N:48065 76 0     281140999 255943600 257104944 311286892 48065 SRX9666706 SRS7865643 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62505 62505 SRR13234621 SRX9666705 SRS7865642 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf untreated polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 bkgd match WT 2h pA AGN001778   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:background matched ythdf2 +/+ or +/ or / |strain maternal:ythdf2 +/ |strain paternal:ythdf2 +/ |molecule:mRNA|selection:pA|sample ref:AGS001424|replicate ref:AGN001778|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 background matched wild type 2hpf untreated polyA AGR002438 AGR002438 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002438_R1.fastq.gz fastq 1063256720.0 13990220.0 AGR002438 R1.fastq.gz 0:76 1:0 A:271493158;C:247048838;G:246969120;T:297698706;N:46898 76 0     271493158 247048838 246969120 297698706 46898 SRX9666705 SRS7865642 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92544   0.03976   0.75842   0.4903   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62506 62506 SRR13234622 SRX9666704 SRS7865641 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf untreated polyA MZythdf2 vs bkgd match WT mRNA pA &amp; R0 rep1 MZythdf2 2h pA AGN001777   strain:TU/AB|age:2.0|dev stage:128 cell 256 cell|sex:pooled male and female|tissue:embryo|genotype:MZythdf2 8/ 8|strain maternal:ythdf2 8/ 8|strain paternal:ythdf2 8/ 8|molecule:mRNA|selection:pA|sample ref:AGS001423|replicate ref:AGN001777|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2 vs bkgd match WT mRNA pA & R0 rep1 MZythdf2 2hpf untreated polyA AGR002437 AGR002437 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR002437_R1.fastq.gz fastq 1062576976.0 13981276.0 AGR002437 R1.fastq.gz 0:76 1:0 A:272735315;C:246274933;G:245836975;T:297683721;N:46032 76 0     272735315 246274933 245836975 297683721 46032 SRX9666704 SRS7865641 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.9197   0.03749   0.76169   0.49147   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62507 62507 SRR13234623 SRX9666703 SRS7865638 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 48h miR 430 pA AGN000156   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000144|replicate ref:AGN000156|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf + miR 430 polyA AGR000210 AGR000210 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000210_R1.fastq.gz fastq 2609702212.0 34338187.0 AGR000210 R1.fastq.gz 0:76 1:0 A:704577933;C:585211587;G:576153508;T:743579979;N:179205 76 0     704577933 585211587 576153508 743579979 179205 SRX9666703 SRS7865638 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93632   0.13425   0.68489   0.46247   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62508 62508 SRR13234624 SRX9666702 SRS7865640 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 48h pA AGN000155   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |molecule:RNA|selection:pA|sample ref:AGS000143|replicate ref:AGN000155|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf polyA AGR000209 AGR000209 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000209_R1.fastq.gz fastq 2762255872.0 36345472.0 AGR000209 R1.fastq.gz 0:76 1:0 A:744803398;C:616941583;G:611018882;T:789301931;N:190078 76 0     744803398 616941583 611018882 789301931 190078 SRX9666702 SRS7865640 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93333   0.1447   0.67556   0.46613   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62509 62509 SRR13234625 SRX9666701 SRS7865639 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 48h miR 430 pA AGN000154   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000142|replicate ref:AGN000154|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf + miR 430 polyA AGR000208 AGR000208 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000208_R1.fastq.gz fastq 2256650140.0 29692765.0 AGR000208 R1.fastq.gz 0:76 1:0 A:605316845;C:506931236;G:499614551;T:644626383;N:161125 76 0     605316845 506931236 499614551 644626383 161125 SRX9666701 SRS7865639 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93484   0.1382   0.68753   0.46979   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62510 62510 SRR13234626 SRX9666700 SRS7865637 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 48h pA AGN000153   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |molecule:RNA|selection:pA|sample ref:AGS000141|replicate ref:AGN000153|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf polyA AGR000207 AGR000207 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000207_R1.fastq.gz fastq 3097923020.0 40762145.0 AGR000207 R1.fastq.gz 0:76 1:0 A:867547957;C:671005273;G:664584552;T:894570865;N:214373 76 0     867547957 671005273 664584552 894570865 214373 SRX9666700 SRS7865637 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92558   0.17346   0.68763   0.47572   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62511 62511 SRR13234627 SRX9666699 SRS7865635 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 48h pA AGN000152   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|molecule:RNA|selection:pA|sample ref:AGS000140|replicate ref:AGN000152|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 48hpf polyA AGR000206 AGR000206 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000206_R1.fastq.gz fastq 2629388112.0 34597212.0 AGR000206 R1.fastq.gz 0:76 1:0 A:705900102;C:587010373;G:584434557;T:751862507;N:180573 76 0     705900102 587010373 584434557 751862507 180573 SRX9666699 SRS7865635 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93679   0.13092   0.68521   0.44617   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62512 62512 SRR13234628 SRX9666698 SRS7865636 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + alpha amanitin + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 6h shield a Am miR 430 pA AGN000133   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:alpha amanitin miR 430|molecule:RNA|selection:pA|sample ref:AGS000121|replicate ref:AGN000133|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + alpha amanitin + miR 430 polyA AGR000187 AGR000187 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000187_R1.fastq.gz fastq 2631852716.0 34629641.0 AGR000187 R1.fastq.gz 0:76 1:0 A:694722114;C:608051504;G:592006258;T:736477995;N:594845 76 0     694722114 608051504 592006258 736477995 594845 SRX9666698 SRS7865636 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94914   0.0523   0.79001   0.49444   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62513 62513 SRR13234629 SRX9666697 SRS7865633 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 24h miR 430 pA AGN000151   strain:TU/AB|age:24.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000139|replicate ref:AGN000151|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf + miR 430 polyA AGR000205 AGR000205 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000205_R1.fastq.gz fastq 2727788580.0 35891955.0 AGR000205 R1.fastq.gz 0:76 1:0 A:729356309;C:615469895;G:605441208;T:777367849;N:153319 76 0     729356309 615469895 605441208 777367849 153319 SRX9666697 SRS7865633 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94092   0.11617   0.69812   0.46621   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Multi-stage Embryo Embryo Imprecise All anatomical structures
62514 62514 SRR13234630 SRX9666696 SRS7865634 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 24h pA AGN000150   strain:TU/AB|age:24.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |molecule:RNA|selection:pA|sample ref:AGS000138|replicate ref:AGN000150|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 24hpf polyA AGR000204 AGR000204 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000204_R1.fastq.gz fastq 2636487272.0 34690622.0 AGR000204 R1.fastq.gz 0:76 1:0 A:711904145;C:590614495;G:581863191;T:751960867;N:144574 76 0     711904145 590614495 581863191 751960867 144574 SRX9666696 SRS7865634 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93765   0.12096   0.69187   0.47423   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Multi-stage Embryo Embryo Imprecise All anatomical structures
62515 62515 SRR13234631 SRX9666695 SRS7865632 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 24h miR 430 pA AGN000149   strain:TU/AB|age:24.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000137|replicate ref:AGN000149|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf + miR 430 polyA AGR000203 AGR000203 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000203_R1.fastq.gz fastq 2458941240.0 32354490.0 AGR000203 R1.fastq.gz 0:76 1:0 A:658826404;C:554609294;G:545318725;T:700047186;N:139631 76 0     658826404 554609294 545318725 700047186 139631 SRX9666695 SRS7865632 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93305   0.12726   0.69229   0.47229   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Multi-stage Embryo Embryo Imprecise All anatomical structures
62516 62516 SRR13234632 SRX9666694 SRS7865631 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 24h pA AGN000148   strain:TU/AB|age:24.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |molecule:RNA|selection:pA|sample ref:AGS000136|replicate ref:AGN000148|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 24hpf polyA AGR000202 AGR000202 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000202_R1.fastq.gz fastq 2774787284.0 36510359.0 AGR000202 R1.fastq.gz 0:76 1:0 A:764934757;C:611096752;G:604464623;T:794135162;N:155990 76 0     764934757 611096752 604464623 794135162 155990 SRX9666694 SRS7865631 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92824   0.15268   0.70485   0.48175   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Multi-stage Embryo Embryo Imprecise All anatomical structures
62517 62517 SRR13234633 SRX9666693 SRS7865629 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 24hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 24h pA AGN000147   strain:TU/AB|age:24.0|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|molecule:RNA|selection:pA|sample ref:AGS000135|replicate ref:AGN000147|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 24hpf polyA AGR000201 AGR000201 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000201_R1.fastq.gz fastq 2742017604.0 36079179.0 AGR000201 R1.fastq.gz 0:76 1:0 A:730482205;C:622643706;G:610359881;T:778376331;N:155481 76 0     730482205 622643706 610359881 778376331 155481 SRX9666693 SRS7865629 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94286   0.103   0.69798   0.47058   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Multi-stage Embryo Embryo Imprecise All anatomical structures
62518 62518 SRR13234634 SRX9666692 SRS7865630 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 6hpf shield + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 6h shield miR 430 pA AGN000146   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000134|replicate ref:AGN000146|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 6hpf shield + miR 430 polyA AGR000200 AGR000200 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000200_R1.fastq.gz fastq 3919751224.0 51575674.0 AGR000200 R1.fastq.gz 0:76 1:0 A:1081009237;C:874549155;G:855765442;T:1108099190;N:328200 76 0     1081009237 874549155 855765442 1108099190 328200 SRX9666692 SRS7865630 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94118   0.10939   0.74878   0.4731   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62519 62519 SRR13234635 SRX9666691 SRS7865626 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type + tinyLNA miR 430 6hpf shield ribo0 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT tinyLNA miR 430 6h shield r0 AGN000145   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:tinyLNA for miR 430|molecule:RNA|selection:r0|sample ref:AGS000133|replicate ref:AGN000145|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type + tinyLNA miR 430 6hpf shield ribo0 AGR000199 AGR000199 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000199_R1.fastq.gz fastq 3973389592.0 52281442.0 AGR000199 R1.fastq.gz 0:76 1:0 A:732379950;C:1180161072;G:1218688247;T:841847667;N:312656 76 0     732379950 1180161072 1218688247 841847667 312656 SRX9666691 SRS7865626 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.66604   0.19006   0.78289   0.48187   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62520 62520 SRR13234636 SRX9666690 SRS7865627 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 6hpf shield + miR 430 ribo0 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdicer 6h shield miR 430 r0 AGN000144   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |treatment:miR 430|molecule:RNA|selection:r0|sample ref:AGS000132|replicate ref:AGN000144|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 6hpf shield + miR 430 ribo0 AGR000198 AGR000198 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000198_R1.fastq.gz fastq 3115354228.0 40991503.0 AGR000198 R1.fastq.gz 0:76 1:0 A:640326782;C:871847094;G:886326760;T:716596262;N:257330 76 0     640326782 871847094 886326760 716596262 257330 SRX9666690 SRS7865627 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.71292   0.22331   0.77279   0.48198   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62521 62521 SRR13234637 SRX9666689 SRS7865625 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + alpha amanitin + miR 430 ribo0 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 6h shield a Am miR 430 r0 AGN000141   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:alpha amanitin miR 430|molecule:RNA|selection:r0|sample ref:AGS000129|replicate ref:AGN000141|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield + alpha amanitin + miR 430 ribo0 AGR000195 AGR000195 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000195_R1.fastq.gz fastq 2883009308.0 37934333.0 AGR000195 R1.fastq.gz 0:76 1:0 A:467440975;C:912630541;G:943060020;T:559716909;N:160863 76 0     467440975 912630541 943060020 559716909 160863 SRX9666689 SRS7865625 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.53568   0.07859   0.82252   0.4774   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62522 62522 SRR13234638 SRX9666688 SRS7865628 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield ribo0 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT 6h shield r0 AGN000139   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|molecule:RNA|selection:r0|sample ref:AGS000127|replicate ref:AGN000139|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 6hpf shield ribo0 AGR000193 AGR000193 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000193_R1.fastq.gz fastq 3157474872.0 41545722.0 AGR000193 R1.fastq.gz 0:76 1:0 A:688624391;C:843991444;G:847459419;T:777217230;N:182388 76 0     688624391 843991444 847459419 777217230 182388 SRX9666688 SRS7865628 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.75413   0.23936   0.76203   0.48275   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62523 62523 SRR13234639 SRX9666687 SRS7865623 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6hpf polyA MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO WT 6h pA AGN002374   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:pA|sample ref:AGS001801|replicate ref:AGN002374|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6hpf polyA AGR003066 AGR003066 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003066_R1.fastq.gz fastq 310682528.0 4087928.0 AGR003066 R1.fastq.gz 0:76 1:0 A:76757310;C:72866929;G:70862687;T:90189770;N:5832 76 0     76757310 72866929 70862687 90189770 5832 SRX9666687 SRS7865623 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94297   0.13518   0.75386   0.55837   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62524 62524 SRR13234640 SRX9666686 SRS7865624 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO WT 6h r0 AGN002373   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:r0|sample ref:AGS001800|replicate ref:AGN002373|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6hpf ribo0 AGR003065 AGR003065 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003065_R1.fastq.gz fastq 392661448.0 5166598.0 AGR003065 R1.fastq.gz 0:76 1:0 A:73079745;C:120499045;G:129633333;T:69441586;N:7739 76 0     73079745 120499045 129633333 69441586 7739 SRX9666686 SRS7865624 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.95137   0.1502   0.81481   0.7931   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62525 62525 SRR13234641 SRX9666685 SRS7865622 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6.6hpf polyA MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO WT 6.6h pA AGN002372   strain:TU/AB|age:6.6|dev stage:65% epiboly|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:pA|sample ref:AGS001799|replicate ref:AGN002372|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6.6hpf polyA AGR003064 AGR003064 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003064_R1.fastq.gz fastq 310684200.0 4087950.0 AGR003064 R1.fastq.gz 0:76 1:0 A:76440735;C:73135160;G:71316425;T:89785849;N:6031 76 0     76440735 73135160 71316425 89785849 6031 SRX9666685 SRS7865622 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94256   0.14267   0.75897   0.55046   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62526 62526 SRR13234642 SRX9666684 SRS7865621 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6.6hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO WT 6.6h r0 AGN002371   strain:TU/AB|age:6.6|dev stage:65% epiboly|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:r0|sample ref:AGS001798|replicate ref:AGN002371|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO unrelated TUAB wild type untreated 6.6hpf ribo0 AGR003063 AGR003063 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003063_R1.fastq.gz fastq 343437312.0 4518912.0 AGR003063 R1.fastq.gz 0:76 1:0 A:64748585;C:104049860;G:112907736;T:61724622;N:6509 76 0     64748585 104049860 112907736 61724622 6509 SRX9666684 SRS7865621 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94727   0.15112   0.81136   0.7853   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62527 62527 SRR13234643 SRX9666683 SRS7865619 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO background matched ythdf2 het; MZythdf3 control untreated 6hpf polyA MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO bkgd match ythdf2 het; MZythdf3 6h pA AGN002366   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:ythdf2 223/+ or 223/ 223; MZythdf3|strain maternal:ythdf2 223/+; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:pA|sample ref:AGS001793|replicate ref:AGN002366|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO background matched ythdf2 het; MZythdf3 control untreated 6hpf polyA AGR003058 AGR003058 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003058_R1.fastq.gz fastq 298609016.0 3929066.0 AGR003058 R1.fastq.gz 0:76 1:0 A:72683629;C:71702471;G:69286407;T:84930854;N:5655 76 0     72683629 71702471 69286407 84930854 5655 SRX9666683 SRS7865619 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.95074   0.11694   0.7611   0.53042   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62528 62528 SRR13234644 SRX9666682 SRS7865620 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO background matched ythdf2 het; MZythdf3 control untreated 6hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO bkgd match ythdf2 het; MZythdf3 6h r0 AGN002365   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:ythdf2 223/+ or 223/ 223; MZythdf3|strain maternal:ythdf2 223/+; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:r0|sample ref:AGS001792|replicate ref:AGN002365|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO background matched ythdf2 het; MZythdf3 control untreated 6hpf ribo0 AGR003057 AGR003057 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003057_R1.fastq.gz fastq 377598628.0 4968403.0 AGR003057 R1.fastq.gz 0:76 1:0 A:70852134;C:115198962;G:124942835;T:66597850;N:6847 76 0     70852134 115198962 124942835 66597850 6847 SRX9666682 SRS7865620 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.95096   0.1351   0.81357   0.82137   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62529 62529 SRR13234645 SRX9666681 SRS7865618 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6hpf polyA MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO MZythdf2/3 6h pA AGN002364   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:pA|sample ref:AGS001791|replicate ref:AGN002364|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6hpf polyA AGR003056 AGR003056 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003056_R1.fastq.gz fastq 320772516.0 4220691.0 AGR003056 R1.fastq.gz 0:76 1:0 A:78951482;C:75368562;G:73554714;T:92891483;N:6275 76 0     78951482 75368562 73554714 92891483 6275 SRX9666681 SRS7865618 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94245   0.1003   0.7584   0.54633   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62530 62530 SRR13234646 SRX9666680 SRS7865617 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO MZythdf2/3 6h r0 AGN002363   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:r0|sample ref:AGS001790|replicate ref:AGN002363|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6hpf ribo0 AGR003055 AGR003055 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003055_R1.fastq.gz fastq 379618404.0 4994979.0 AGR003055 R1.fastq.gz 0:76 1:0 A:69420279;C:116863059;G:128695072;T:64632933;N:7061 76 0     69420279 116863059 128695072 64632933 7061 SRX9666680 SRS7865617 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.95174   0.11717   0.81675   0.83589   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62531 62531 SRR13234647 SRX9666679 SRS7865616 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 6hpf shield polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 MZdrosha 6h shield pA AGN000138   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |molecule:RNA|selection:pA|sample ref:AGS000126|replicate ref:AGN000138|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 6hpf shield polyA AGR000192 AGR000192 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000192_R1.fastq.gz fastq 3250494996.0 42769671.0 AGR000192 R1.fastq.gz 0:76 1:0 A:880358436;C:726180935;G:715765398;T:928019682;N:170545 76 0     880358436 726180935 715765398 928019682 170545 SRX9666679 SRS7865616 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93732   0.11377   0.75035   0.48262   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62532 62532 SRR13234648 SRX9666678 SRS7865615 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6.6hpf polyA MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO MZythdf2/3 6.6h pA AGN002362   strain:TU/AB|age:6.6|dev stage:65% epiboly|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:pA|sample ref:AGS001789|replicate ref:AGN002362|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6.6hpf polyA AGR003054 AGR003054 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003054_R1.fastq.gz fastq 276739560.0 3641310.0 AGR003054 R1.fastq.gz 0:76 1:0 A:67082784;C:65679468;G:64088852;T:79883445;N:5011 76 0     67082784 65679468 64088852 79883445 5011 SRX9666678 SRS7865615 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.94602   0.11731   0.76572   0.55896   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures
62533 62533 SRR13234649 SRX9666677 SRS7865614 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6.6hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 Ythdf1 MO MZythdf2/3 6.6h r0 AGN002361   strain:TU/AB|age:6.6|dev stage:65% epiboly|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:r0|sample ref:AGS001788|replicate ref:AGN002361|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 Ythdf1 MO MZythdf2;MZythdf3 untreated 6.6hpf ribo0 AGR003053 AGR003053 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina NovaSeq 6000   SRP297464     AGR003053_R1.fastq.gz fastq 364494176.0 4795976.0 AGR003053 R1.fastq.gz 0:76 1:0 A:68004278;C:111137482;G:121348144;T:63997273;N:6999 76 0     68004278 111137482 121348144 63997273 6999 SRX9666677 SRS7865614 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.95149   0.12666   0.81736   0.8253   76   B   usable mapping rate illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Gastrula Embryo Embryo Imprecise All anatomical structures
62534 62534 SRR13234650 SRX9666676 SRS7865613 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 bkgd match ythdf2 het; MZythdf3 0h r0 AGN002340   strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|genotype:ythdf2 223/+ or 223/ 223; MZythdf3|strain maternal:ythdf2 223/+; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:r0|sample ref:AGS001769|replicate ref:AGN002340|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf ribo0 AGR003028 AGR003028 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003028_R1.fastq.gz fastq 809198220.0 10647345.0 AGR003028 R1.fastq.gz 0:76 1:0 A:131548927;C:262799074;G:295723637;T:119078265;N:48317 76 0     131548927 262799074 295723637 119078265 48317 SRX9666676 SRS7865613 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.96134   0.02867   0.81138   0.85893   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Zygote Embryo Embryo Imprecise All anatomical structures
62535 62535 SRR13234651 SRX9666675 SRS7865612 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0h ribo0 MZythdf2/3 mRNA pA &amp; R0 WT 0h r0 AGN002339   strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:r0|sample ref:AGS001768|replicate ref:AGN002339|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0h ribo0 AGR003027 AGR003027 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003027_R1.fastq.gz fastq 935971920.0 12315420.0 AGR003027 R1.fastq.gz 0:76 1:0 A:153283406;C:303473141;G:336325094;T:142833742;N:56537 76 0     153283406 303473141 336325094 142833742 56537 SRX9666675 SRS7865612 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.9604   0.02878   0.80628   0.79692   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Zygote Embryo Embryo Imprecise All anatomical structures
62536 62536 SRR13234652 SRX9666674 SRS7865610 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf ribo0 MZythdf2/3 mRNA pA &amp; R0 MZythdf2; MZythdf3 0h r0 AGN002338   strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:r0|sample ref:AGS001767|replicate ref:AGN002338|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 0hpf ribo0 AGR003026 AGR003026 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003026_R1.fastq.gz fastq 1165630772.0 15337247.0 AGR003026 R1.fastq.gz 0:76 1:0 A:185914121;C:376601239;G:425671246;T:177374359;N:69807 76 0     185914121 376601239 425671246 177374359 69807 SRX9666674 SRS7865610 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.96047   0.02268   0.81377   0.84903   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Zygote Embryo Embryo Imprecise All anatomical structures
62537 62537 SRR13234653 SRX9666673 SRS7865611 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf polyA MZythdf2/3 mRNA pA &amp; R0 bkgd match ythdf2 het; MZythdf3 0h pA AGN002335   strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|genotype:ythdf2 223/+ or 223/ 223; MZythdf3|strain maternal:ythdf2 223/+; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:pA|sample ref:AGS001764|replicate ref:AGN002335|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 background matched ythdf2 het; MZythdf3 control 0hpf polyA AGR003022 AGR003022 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003022_R1.fastq.gz fastq 607989056.0 7999856.0 AGR003022 R1.fastq.gz 0:76 1:0 A:153708086;C:142012326;G:138315448;T:173916462;N:36734 76 0     153708086 142012326 138315448 173916462 36734 SRX9666673 SRS7865611 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92885   0.03117   0.78362   0.5405   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Zygote Embryo Embryo Imprecise All anatomical structures
62538 62538 SRR13234654 SRX9666672 SRS7865609 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 4hpf polyA MZythdf2/3 mRNA pA &amp; R0 WT 4h pA AGN002334   strain:TU/AB|age:4.0|dev stage:sphere|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:pA|sample ref:AGS001763|replicate ref:AGN002334|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 4hpf polyA AGR003021 AGR003021 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003021_R1.fastq.gz fastq 694620240.0 9139740.0 AGR003021 R1.fastq.gz 0:76 1:0 A:176019737;C:161882360;G:156054590;T:200621560;N:41993 76 0     176019737 161882360 156054590 200621560 41993 SRX9666672 SRS7865609 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92422   0.06698   0.74519   0.52801   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62539 62539 SRR13234655 SRX9666671 SRS7865608 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 2hpf polyA MZythdf2/3 mRNA pA &amp; R0 WT 2h pA AGN002333   strain:TU/AB|age:2.0|dev stage:64 cell 128 cell|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:pA|sample ref:AGS001762|replicate ref:AGN002333|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 2hpf polyA AGR003020 AGR003020 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003020_R1.fastq.gz fastq 585244308.0 7700583.0 AGR003020 R1.fastq.gz 0:76 1:0 A:146436207;C:138168832;G:132640929;T:167963204;N:35136 76 0     146436207 138168832 132640929 167963204 35136 SRX9666671 SRS7865608 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93873   0.03373   0.76215   0.51712   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Multi-stage Embryo Embryo Imprecise All anatomical structures
62540 62540 SRR13234656 SRX9666670 SRS7865605 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0hpf polyA MZythdf2/3 mRNA pA &amp; R0 WT 0h pA AGN002332   strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|strain maternal:unrelated TUAB wild type|strain paternal:unrelated TUAB wild type|molecule:mRNA|selection:pA|sample ref:AGS001761|replicate ref:AGN002332|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 unrelated TUAB wild type 0hpf polyA AGR003019 AGR003019 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003019_R1.fastq.gz fastq 565381784.0 7439234.0 AGR003019 R1.fastq.gz 0:76 1:0 A:140209814;C:133250366;G:128677079;T:163209960;N:34565 76 0     140209814 133250366 128677079 163209960 34565 SRX9666670 SRS7865605 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93741   0.04563   0.80144   0.5511   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Zygote Embryo Embryo Imprecise All anatomical structures
62541 62541 SRR13234657 SRX9666669 SRS7865607 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 4hpf polyA MZythdf2/3 mRNA pA &amp; R0 MZythdf2; MZythdf3 4h pA AGN002331   strain:TU/AB|age:4.0|dev stage:1k cell|sex:pooled male and female|tissue:embryo|genotype:MZythdf2; MZythdf3|strain maternal:ythdf2 223/ 223; ythdf3 365/ 365|strain paternal:ythdf2 223/ 223; ythdf3 365/ 365|molecule:mRNA|selection:pA|sample ref:AGS001760|replicate ref:AGN002331|replicate order:1|BioSampleModel:Model organism or animal                 MZythdf2/3 mRNA pA & R0 MZythdf2; MZythdf3 4hpf polyA AGR003018 AGR003018 mRNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500   SRP297464     AGR003018_R1.fastq.gz fastq 743665852.0 9785077.0 AGR003018 R1.fastq.gz 0:76 1:0 A:192601267;C:170018208;G:165679412;T:215322088;N:44877 76 0     192601267 170018208 165679412 215322088 44877 SRX9666669 SRS7865607 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92433   0.07573   0.74759   0.53218   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-09 Blastula Embryo Embryo Imprecise All anatomical structures
62542 62542 SRR13234658 SRX9666668 SRS7865606 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type + tinyLNA miR 430 6hpf shield polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA &amp; R0 WT tinyLNA miR 430 6h shield pA AGN000137   strain:TU/AB|age:6.0|dev stage:shield|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|treatment:tinyLNA for miR 430|molecule:RNA|selection:pA|sample ref:AGS000125|replicate ref:AGN000137|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type + tinyLNA miR 430 6hpf shield polyA AGR000191 AGR000191 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000191_R1.fastq.gz fastq 3401483056.0 44756356.0 AGR000191 R1.fastq.gz 0:76 1:0 A:908201805;C:765108874;G:751863503;T:976132401;N:176473 76 0     908201805 765108874 751863503 976132401 176473 SRX9666668 SRS7865606 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.934   0.13092   0.7497   0.48158   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Gastrula Embryo Embryo Imprecise All anatomical structures

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