{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Zygote\" and experiment.library_selection = \"unspecified\"", "rows": [[51155, "SRR8552547", "SRX5354343", "SRS4345561", "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.", null, null, null, "RPF   WT 0h Cycloheximide Ribo  RPF", "RPF   WT 0h CHX R  RPF AGN000073", null, "strain:TU/AB|age:0.0|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:cyclohex|molecule:RNA|selection:r |condition:RPF|sample ref:AGS000069|replicate ref:AGN000073|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RPF   WT 0h Cycloheximide Ribo  RPF", "AGR000135", "AGR000135", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP184786", null, null, "AGR000135_R1.fastq.gz", "fastq", 2161849320.0, 30025685.0, "AGR000135 R1.fastq.gz", "0:72", "A:645981607;C:467229372;G:514731353;T:527710797;N:6196191", 72, null, null, null, 645981607, 467229372, 514731353, 527710797, 6196191, "SRX5354343", "SRS4345561", "SRA847217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 72, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-02-08", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51621, "SRR8788632", "SRX5578491", "SRS4540272", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT 1c R0 B2", "Developmental timecourse   WT 1c R0 B2 AGN000663", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000583|replicate ref:AGN000663|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT 1c R0 B2", "AGR000855", "AGR000855", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000855_R1.fastq.gz AGR000855_R2.fastq.gz", "fastq fastq", 2435568352.0, 16023476.0, "AGR000855 R1.fastq.gz", "0:76 1:76", "A:629791020;C:590108147;G:587059372;T:624338627;N:4271186", 76, 76, null, null, 629791020, 590108147, 587059372, 624338627, 4271186, "SRX5578491", "SRS4540272", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.87561, 0.86738, 0.07392, 0.07503, 0.76266, 0.76102, 0.46339, 0.46911, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51622, "SRR8788633", "SRX5578490", "SRS4540271", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT 1c R0 B1", "Developmental timecourse   WT 1c R0 B1 AGN000662", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:r0|sample ref:AGS000583|replicate ref:AGN000662|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT 1c R0 B1", "AGR000854", "AGR000854", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000854_R1.fastq.gz AGR000854_R2.fastq.gz", "fastq fastq", 2337549024.0, 15378612.0, "AGR000854 R1.fastq.gz", "0:76 1:76", "A:609210481;C:563729049;G:558514098;T:602041398;N:4053998", 76, 76, null, null, 609210481, 563729049, 558514098, 602041398, 4053998, "SRX5578490", "SRS4540271", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.88449, 0.87899, 0.06047, 0.0611, 0.7601, 0.75838, 0.47133, 0.47598, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51637, "SRR8788648", "SRX5578475", "SRS4540259", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT 1c pA B1", "Developmental timecourse   WT 1c pA B1 AGN000636", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000570|replicate ref:AGN000636|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT 1c pA B1", "AGR000828", "AGR000828", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000828_R1.fastq.gz AGR000828_R2.fastq.gz", "fastq fastq", 1778932000.0, 11703500.0, "AGR000828 R1.fastq.gz", "0:76 1:76", "A:473620191;C:414842330;G:414924231;T:473971099;N:1574149", 76, 76, null, null, 473620191, 414842330, 414924231, 473971099, 1574149, "SRX5578475", "SRS4540259", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.93194, 0.93539, 0.02446, 0.02342, 0.81671, 0.81696, 0.48421, 0.48694, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51638, "SRR8788649", "SRX5578474", "SRS4540258", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT 1c pA B2", "Developmental timecourse   WT 1c pA B2 AGN000637", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|sample ref:AGS000570|replicate ref:AGN000637|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT 1c pA B2", "AGR000829", "AGR000829", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000829_R1.fastq.gz AGR000829_R2.fastq.gz", "fastq fastq", 2327471424.0, 15312312.0, "AGR000829 R1.fastq.gz", "0:76 1:76", "A:617481287;C:543018300;G:545498739;T:619434178;N:2038920", 76, 76, null, null, 617481287, 543018300, 545498739, 619434178, 2038920, "SRX5578474", "SRS4540258", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.92019, 0.92287, 0.02435, 0.02357, 0.81426, 0.8145, 0.48095, 0.48594, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51647, "SRR8788658", "SRX5578465", "SRS4540254", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c pA B2", "Developmental timecourse   WT a Am 1c pA B2 AGN000689", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|sample ref:AGS000596|replicate ref:AGN000689|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c pA B2", "AGR000901", "AGR000901", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000901_R1.fastq.gz AGR000901_R2.fastq.gz", "fastq fastq", 2702532792.0, 17779821.0, "AGR000901 R1.fastq.gz", "0:76 1:76", "A:716369155;C:635020541;G:634097644;T:714669224;N:2376228", 76, 76, null, null, 716369155, 635020541, 634097644, 714669224, 2376228, "SRX5578465", "SRS4540254", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.92422, 0.92692, 0.02266, 0.02137, 0.82481, 0.82495, 0.49869, 0.50166, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51669, "SRR8788680", "SRX5578443", "SRS4540236", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c pA B1", "Developmental timecourse   WT a Am 1c pA B1 AGN000688", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:pA|sample ref:AGS000596|replicate ref:AGN000688|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c pA B1", "AGR000900", "AGR000900", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000900_R1.fastq.gz AGR000900_R2.fastq.gz", "fastq fastq", 2460261056.0, 16185928.0, "AGR000900 R1.fastq.gz", "0:76 1:76", "A:657092605;C:573296643;G:571761179;T:655966705;N:2143924", 76, 76, null, null, 657092605, 573296643, 571761179, 655966705, 2143924, "SRX5578443", "SRS4540236", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.91111, 0.91731, 0.02394, 0.02269, 0.8269, 0.82747, 0.4987, 0.49478, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51671, "SRR8788682", "SRX5578441", "SRS4540219", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c R0 B2", "Developmental timecourse   WT a Am 1c R0 B2 AGN000705", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:r0|sample ref:AGS000604|replicate ref:AGN000705|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c R0 B2", "AGR000919", "AGR000919", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000919_R1.fastq.gz AGR000919_R2.fastq.gz", "fastq fastq", 4296568800.0, 28266900.0, "AGR000919 R1.fastq.gz", "0:76 1:76", "A:1116113844;C:1001549711;G:1051044551;T:1119953961;N:7906733", 76, 76, null, null, 1116113844, 1001549711, 1051044551, 1119953961, 7906733, "SRX5578441", "SRS4540219", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.61505, 0.62079, 0.11845, 0.11395, 0.7878, 0.79273, 0.52552, 0.5261, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51694, "SRR8788705", "SRX5578418", "SRS4540219", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c R0 B2", "Developmental timecourse   WT a Am 1c R0 B2 AGN000705", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:r0|sample ref:AGS000604|replicate ref:AGN000705|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c R0 B2", "AGR000918", "AGR000918", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000918_R1.fastq.gz AGR000918_R2.fastq.gz", "fastq fastq", 2356801040.0, 15505270.0, "AGR000918 R1.fastq.gz", "0:76 1:76", "A:645305534;C:504536913;G:529941536;T:671927563;N:5089494", 76, 76, null, null, 645305534, 504536913, 529941536, 671927563, 5089494, "SRX5578418", "SRS4540219", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.66091, 0.63258, 0.1287, 0.13224, 0.78715, 0.79109, 0.53729, 0.53151, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51695, "SRR8788706", "SRX5578417", "SRS4540217", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c R0 B1", "Developmental timecourse   WT a Am 1c R0 B1 AGN000704", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:r0|sample ref:AGS000604|replicate ref:AGN000704|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c R0 B1", "AGR000917", "AGR000917", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000917_R1.fastq.gz AGR000917_R2.fastq.gz", "fastq fastq", 3129506568.0, 20588859.0, "AGR000917 R1.fastq.gz", "0:76 1:76", "A:805704877;C:741159058;G:771769886;T:805184484;N:5688263", 76, 76, null, null, 805704877, 741159058, 771769886, 805184484, 5688263, "SRX5578417", "SRS4540217", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.57337, 0.57983, 0.13988, 0.13406, 0.79204, 0.80105, 0.51447, 0.53836, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51696, "SRR8788707", "SRX5578416", "SRS4540217", "SRP189512", "PRJNA529241", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: Developmental mRNA seq timecourse", "PRJNA529241", "Other", "Post transcriptional regulation plays a crucial role in shaping gene expression. During the Maternal to Zygotic Transition MZT  thousands of maternal transcripts are regulated  however  how different cis elements and trans factors are integrated to determine mRNA stability is still poorly understood. Here  we show that most transcripts are under combinatorial regulation by multiple decay pathways during zebrafish MZT. Using a massively parallel reporter assay  we identified cis regulatory sequences in the three prime UTR  including poly U motifs that are associated with mRNA stability. In contrast  miR 430 target sequences  UAUUUAUU AU rich elements ARE  CCUC and CUGC elements emerged as destabilizing motifs  with miR 430 and AREs causing mRNA deadenylation upon genome activation. We identified trans factors by profiling RNA protein interactions and found that poly U binding proteins are preferentially associated with three prime UTR sequences and stabilizing motifs. We demonstrate that this activity is antagonized by poly C motifs and correlated with protein binding. Finally  we integrated these regulatory motifs into a machine learning model that predicts reporter mRNA stability in vivo.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT a Am 1c R0 B1", "Developmental timecourse   WT a Am 1c R0 B1 AGN000704", null, "strain:TU/AB|age:0.2|dev stage:1cell|sex:pooled male and female|tissue:embryo|treatment:alpha am|molecule:RNA|selection:r0|sample ref:AGS000604|replicate ref:AGN000704|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT a Am 1c R0 B1", "AGR000916", "AGR000916", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189512", null, null, "AGR000916_R1.fastq.gz AGR000916_R2.fastq.gz", "fastq fastq", 2105467064.0, 13851757.0, "AGR000916 R1.fastq.gz", "0:76 1:76", "A:578198310;C:450780203;G:468988474;T:603073355;N:4426722", 76, 76, null, null, 578198310, 450780203, 468988474, 603073355, 4426722, "SRX5578416", "SRS4540217", "SRA866166", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.64483, 0.60666, 0.15301, 0.15391, 0.79091, 0.79651, 0.51017, 0.51384, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   background matched ythdf2 het; MZythdf3 control  0hpf ribo0", "MZythdf2/3 mRNA  pA & R0   bkgd match ythdf2 het; MZythdf3 0h r0 AGN002340", null, "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", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   background matched ythdf2 het; MZythdf3 control  0hpf ribo0", "AGR003028", "AGR003028", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "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, null, null, 131548927, 262799074, 295723637, 119078265, 48317, "SRX9666676", "SRS7865613", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96134, null, 0.02867, null, 0.81138, null, 0.85893, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-10", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   unrelated TUAB wild type 0h ribo0", "MZythdf2/3 mRNA  pA & R0   WT 0h r0 AGN002339", null, "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", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   unrelated TUAB wild type 0h ribo0", "AGR003027", "AGR003027", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "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, null, null, 153283406, 303473141, 336325094, 142833742, 56537, "SRX9666675", "SRS7865612", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9604, null, 0.02878, null, 0.80628, null, 0.79692, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-10", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0hpf ribo0", "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0h r0 AGN002338", null, "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", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0hpf ribo0", "AGR003026", "AGR003026", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "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, null, null, 185914121, 376601239, 425671246, 177374359, 69807, "SRX9666674", "SRS7865610", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96047, null, 0.02268, null, 0.81377, null, 0.84903, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-10", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   background matched ythdf2 het; MZythdf3 control  0hpf polyA", "MZythdf2/3 mRNA  pA & R0   bkgd match ythdf2 het; MZythdf3 0h pA AGN002335", null, "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", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   background matched ythdf2 het; MZythdf3 control  0hpf polyA", "AGR003022", "AGR003022", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "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, null, null, 153708086, 142012326, 138315448, 173916462, 36734, "SRX9666673", "SRS7865611", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92885, null, 0.03117, null, 0.78362, null, 0.5405, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-09", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   unrelated TUAB wild type 0hpf polyA", "MZythdf2/3 mRNA  pA & R0   WT 0h pA AGN002332", null, "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", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   unrelated TUAB wild type 0hpf polyA", "AGR003019", "AGR003019", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "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, null, null, 140209814, 133250366, 128677079, 163209960, 34565, "SRX9666670", "SRS7865605", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.93741, null, 0.04563, null, 0.80144, null, 0.5511, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-09", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [62544, "SRR13234660", "SRX9666666", "SRS7865603", "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.", null, null, null, "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0hpf polyA", "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0h pA AGN002329", null, "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:pA|sample ref:AGS001758|replicate ref:AGN002329|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "MZythdf2/3 mRNA  pA & R0   MZythdf2; MZythdf3 0hpf polyA", "AGR003016", "AGR003016", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP297464", null, null, "AGR003016_R1.fastq.gz", "fastq", 695309104.0, 9148804.0, "AGR003016 R1.fastq.gz", "0:76 1:0", "A:179833613;C:157023961;G:155652114;T:202756408;N:43008", 76, 0, null, null, 179833613, 157023961, 155652114, 202756408, 43008, "SRX9666666", "SRS7865603", "SRA1169659", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.93546, null, 0.03548, null, 0.80087, null, 0.5919, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-12-09", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68606, "SRR18052577", "SRX14204750", "SRS12026894", "SRP360172", "PRJNA807674", "A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb", "PRJNA807674", "Other", "The Balbiani body Bb is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects  fish  amphibians  and mammals. During early zebrafish oogenesis  the Bb assembles as a transient aggregate of mRNA  proteins  and membrane bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops  the Bb appears to grow slowly  until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs  this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable  solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity  little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles  translocates  and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample  including known Bb proteins and novel RNA binding proteins. In particular  we identified Cirbpa and Cirbpb  which have both an RNA binding domain and a predicted self aggregation domain. In stage I oocytes  Cirbpa and Cirbpb localize to the Bb rather than the nucleus as in somatic cells  indicating that they may have a specialized function in the germ line. Both the RNA binding domain and the self aggregation domain are sufficient to localize to the Bb  suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb  our proteomics dataset presents many candidates for further study  making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level.", null, null, null, "Oocyte development   Oocyte stage 1.3 40 70\u03bcm 7/14/14 Biorep2", "Oocyte development   Oocyte I.3 B2 AGN001112", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000972|replicate ref:AGN001112|replicate order:2|project label long:Zebrafish oocyte development from Mullins Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.3|replicate label short:Oocyte I.3 B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage 1.3 40 70m 7/14/14 Biorep2", "AGR001536", "AGR001536", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360172", null, null, "AGR001536_R1.fastq.gz", "fastq", 467635448.0, 6153098.0, "AGR001536 R1.fastq.gz", "0:76 1:0", "A:123171986;C:108126001;G:105088073;T:125086357;N:6163031", 76, 0, null, null, 123171986, 108126001, 105088073, 125086357, 6163031, "SRX14204750", "SRS12026894", "SRA1373771", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96741, null, 0.02607, null, 0.7763, null, 0.49394, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68607, "SRR18052578", "SRX14204749", "SRS12026893", "SRP360172", "PRJNA807674", "A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb", "PRJNA807674", "Other", "The Balbiani body Bb is the first marker of polarity in vertebrate oocytes. The Bb is a conserved structure found in diverse animals including insects  fish  amphibians  and mammals. During early zebrafish oogenesis  the Bb assembles as a transient aggregate of mRNA  proteins  and membrane bound organelles at the presumptive vegetal side of the oocyte. As the early oocyte develops  the Bb appears to grow slowly  until at the end of stage I of oogenesis it disassembles and deposits its cargo of localized mRNAs and proteins. In fish and frogs  this cargo includes the germ plasm as well as gene products required to specify dorsal tissues of the future embryo. We demonstrate that the Bb is a stable  solid structure that forms a size exclusion barrier similar to other biological hydrogels. Despite its central role in oocyte polarity  little is known about the mechanism behind the Bb's action. Analysis of the few known protein components of the Bb is insufficient to explain how the Bb assembles  translocates  and disassembles. We isolated Bbs from zebrafish oocytes and performed mass spectrometry to define the Bb proteome. We successfully identified 77 proteins associated with the Bb sample  including known Bb proteins and novel RNA binding proteins. In particular  we identified Cirbpa and Cirbpb  which have both an RNA binding domain and a predicted self aggregation domain. In stage I oocytes  Cirbpa and Cirbpb localize to the Bb rather than the nucleus as in somatic cells  indicating that they may have a specialized function in the germ line. Both the RNA binding domain and the self aggregation domain are sufficient to localize to the Bb  suggesting that Cirbpa and Cirbpb interact with more than just their mRNA targets within the Bb. We propose that Cirbp proteins crosslink mRNA cargo and proteinaceous components of the Bb as it grows. Beyond Cirbpa and Cirbpb  our proteomics dataset presents many candidates for further study  making it a valuable resource for building a comprehensive mechanism for Bb function at a protein level.", null, null, null, "Oocyte development   Oocyte stage I.3 40 70\u03bcm 7/14/14 Biorep1", "Oocyte development   Oocyte I.3 B1 AGN001111", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000972|replicate ref:AGN001111|replicate order:1|project label long:Zebrafish oocyte development from Mullins Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.3|replicate label short:Oocyte I.3 B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage I.3 40 70m 7/14/14 Biorep1", "AGR001535", "AGR001535", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360172", null, null, "AGR001535_R1.fastq.gz", "fastq", 495577380.0, 6520755.0, "AGR001535 R1.fastq.gz", "0:76 1:0", "A:128639721;C:114539094;G:112745153;T:133122222;N:6531190", 76, 0, null, null, 128639721, 114539094, 112745153, 133122222, 6531190, "SRX14204749", "SRS12026893", "SRA1373771", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96355, null, 0.02609, null, 0.76694, null, 0.47874, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68630, "SRR18054176", "SRX14206224", "SRS12028356", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage III >300\u03bcm 7/18/14 Biorep2", "Oocyte development   Oocyte III B2 AGN001118", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000976|replicate ref:AGN001118|replicate order:2|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte III|replicate label short:Oocyte III B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage III >300m 7/18/14 Biorep2", "AGR001530", "AGR001530", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001530_R1.fastq.gz", "fastq", 517403516.0, 6807941.0, "AGR001530 R1.fastq.gz", "0:76 1:0", "A:130410978;C:120266868;G:121067507;T:138839131;N:6819032", 76, 0, null, null, 130410978, 120266868, 121067507, 138839131, 6819032, "SRX14206224", "SRS12028356", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96922, null, 0.02991, null, 0.75519, null, 0.46295, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68631, "SRR18054177", "SRX14206223", "SRS12028357", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage III >300\u03bcm 7/18/14 Biorep1", "Oocyte development   Oocyte III B1 AGN001117", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000976|replicate ref:AGN001117|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte III|replicate label short:Oocyte III B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage III >300m 7/18/14 Biorep1", "AGR001529", "AGR001529", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001529_R1.fastq.gz", "fastq", 533176860.0, 7015485.0, "AGR001529 R1.fastq.gz", "0:76 1:0", "A:134362652;C:123935022;G:124704799;T:143147744;N:7026643", 76, 0, null, null, 134362652, 123935022, 124704799, 143147744, 7026643, "SRX14206223", "SRS12028357", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96834, null, 0.02909, null, 0.75666, null, 0.46022, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68632, "SRR18054178", "SRX14206222", "SRS12028355", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage II 100 300\u03bcm 7/19/14 Biorep2", "Oocyte development   Oocyte II B2 AGN001114", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000974|replicate ref:AGN001114|replicate order:2|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte II|replicate label short:Oocyte II B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage II 100 300m 7/19/14 Biorep2", "AGR001538", "AGR001538", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001538_R1.fastq.gz", "fastq", 506265108.0, 6661383.0, "AGR001538 R1.fastq.gz", "0:76 1:0", "A:130859707;C:117220375;G:114714386;T:136798614;N:6672026", 76, 0, null, null, 130859707, 117220375, 114714386, 136798614, 6672026, "SRX14206222", "SRS12028355", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96292, null, 0.03541, null, 0.75605, null, 0.47042, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68633, "SRR18054179", "SRX14206221", "SRS12028354", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage II 100 300\u03bcm 7/16/14 Biorep1", "Oocyte development   Oocyte II B1 AGN001113", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000974|replicate ref:AGN001113|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte II|replicate label short:Oocyte II B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage II 100 300m 7/16/14 Biorep1", "AGR001537", "AGR001537", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001537_R1.fastq.gz", "fastq", 450099360.0, 5922360.0, "AGR001537 R1.fastq.gz", "0:76 1:0", "A:117120225;C:103500083;G:101671751;T:121875501;N:5931800", 76, 0, null, null, 117120225, 103500083, 101671751, 121875501, 5931800, "SRX14206221", "SRS12028354", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96171, null, 0.03386, null, 0.75635, null, 0.47167, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68634, "SRR18054180", "SRX14206220", "SRS12028352", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage I.2 20 40\u03bcm 7/11/14 Biorep2", "Oocyte development   Oocyte I.2 B2 AGN001110", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000970|replicate ref:AGN001110|replicate order:2|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.2|replicate label short:Oocyte I.2 B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage I.2 20 40m 7/11/14 Biorep2", "AGR001534", "AGR001534", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001534_R1.fastq.gz", "fastq", 522974164.0, 6881239.0, "AGR001534 R1.fastq.gz", "0:76 1:0", "A:136675382;C:120732318;G:119005486;T:139668537;N:6892441", 76, 0, null, null, 136675382, 120732318, 119005486, 139668537, 6892441, "SRX14206220", "SRS12028352", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96408, null, 0.02945, null, 0.7781, null, 0.48418, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68635, "SRR18054181", "SRX14206219", "SRS12028353", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage I.2 20 40\u03bcm 7/11/14 Biorep1", "Oocyte development   Oocyte I.2 B1 AGN001109", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000970|replicate ref:AGN001109|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.2|replicate label short:Oocyte I.2 B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage I.2 20 40m 7/11/14 Biorep1", "AGR001533", "AGR001533", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001533_R1.fastq.gz", "fastq", 454518152.0, 5980502.0, "AGR001533 R1.fastq.gz", "0:76 1:0", "A:120919123;C:103646258;G:100584120;T:123378628;N:5990023", 76, 0, null, null, 120919123, 103646258, 100584120, 123378628, 5990023, "SRX14206219", "SRS12028353", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.96396, null, 0.03175, null, 0.79019, null, 0.51458, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68636, "SRR18054182", "SRX14206218", "SRS12028351", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage I.1 10 20\u03bcm 7/9/14 Biorep2", "Oocyte development   Oocyte I.1 B2 AGN001108", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000968|replicate ref:AGN001108|replicate order:2|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.1|replicate label short:Oocyte I.1 B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage I.1 10 20m 7/9/14 Biorep2", "AGR001532", "AGR001532", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001532_R1.fastq.gz", "fastq", 482678432.0, 6351032.0, "AGR001532 R1.fastq.gz", "0:76 1:0", "A:125959724;C:109945632;G:110752110;T:129659869;N:6361097", 76, 0, null, null, 125959724, 109945632, 110752110, 129659869, 6361097, "SRX14206218", "SRS12028351", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9545, null, 0.05008, null, 0.75158, null, 0.49904, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68637, "SRR18054183", "SRX14206217", "SRS12028350", "SRP360207", "PRJNA807702", "Stage specific transcriptomic analysis and database for zebrafish oogenesis", "PRJNA807702", "Other", "Oogenesis produces functional eggs and is essential for fertility  embryonic development and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates  and recent studies have identified multiple regulators in oocyte development through forward genetics screens  as well as reverse genetics by CRISPR mutagenesis. However  many developmental steps in oogenesis  in zebrafish and other species  remain poorly understood  and their underlying mechanisms are unknown. Here  we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis  from the onset of oocyte differentiation through the premature egg. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis  as well as their expression in pair wise comparisons between stages. We determined their functionally enriched terms  identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish  which we deposit online as a resource for the community. Further  the presence of multiple gene isoforms in zebrafish  and the exclusive curation of the single isoforms present in humans by many bioinformatic tools  challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether  our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.", null, null, null, "Oocyte development   Oocyte stage I.1 10 20\u03bcm 7/9/14 Biorep1", "Oocyte development   Oocyte I.1 B1 AGN001107", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|molecule:mRNA|selection:pA|sample ref:AGS000968|replicate ref:AGN001107|replicate order:1|project label long:Zebrafish oocyte development from Mullins/Elkouby Lab sorted cells|project label short:Oocyte development|sample label short:Oocyte I.1|replicate label short:Oocyte I.1 B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Oocyte development   Oocyte stage I.1 10 20m 7/9/14 Biorep1", "AGR001531", "AGR001531", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP360207", null, null, "AGR001531_R1.fastq.gz", "fastq", 495339804.0, 6517629.0, "AGR001531 R1.fastq.gz", "0:76 1:0", "A:130381117;C:112367825;G:112982326;T:133080550;N:6527986", 76, 0, null, null, 130381117, 112367825, 112982326, 133080550, 6527986, "SRX14206217", "SRS12028350", "SRA1373868", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94462, null, 0.05195, null, 0.7486, null, 0.51364, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2022-02-21", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 27, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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