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CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   embryo prim6 stage", "D. rerio prim6 embryo", "D. rerio prim6 embryo", null, null, null, null, null, null, null, null, null, null, "RNAseq   D. rerio prim6 embryo", "RNAseq   D. rerio prim6 embryo", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, "RNAseq_prim6_2_fix.fastq", "fastq", 3011340704.0, 19811452.0, "RNAseq   D. rerio prim6 embryo", "0:76 1:76", "A:727345664;C:767747833;G:787766862;T:725606403;N:2873942", 76, 76, null, null, 727345664, 767747833, 787766862, 725606403, 2873942, "SRX180750", "SRS347212", "SRA055273", "University of Bergen", "ZEPROME consortium", 2, 0.94491, 0.94492, 0.04196, 0.04323, 0.76641, 0.76928, 0.48087, 0.48787, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-22", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, "1", "Test", "GFP Negative 1", null, null, null, null, null, null, null, null, null, null, "Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development", "Embryos", "1", "1", null, null, "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", null, null, null, null, 2525199228.0, 65962848.0, "GFP Positive", "0:38.28", "A:665802914;C:594493287;G:612298433;T:652078696;N:525898", 38, null, null, null, 665802914, 594493287, 612298433, 652078696, 525898, "SRX195432", "SRS369361", null, null, "University of Cambridge", 1, 0.89062, null, 0.09595, null, 0.74059, null, 0.47506, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-07-22", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, "1", "Test", "GFP Negative 1", null, null, null, null, null, null, null, null, null, null, "Global analysis of the haematopoietic and endothelial transcriptome during zebrafish development", "Embryos", "1", "1", null, null, "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", null, null, "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, null, null, null, 686329592, 587342682, 601330559, 674194074, 485241, "SRX195432", "SRS369361", null, null, "University of Cambridge", 1, 0.90413, null, 0.13272, null, 0.71342, null, 0.48186, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2015-07-22", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36586, "SRR1562528", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 3901027000.0, 41246200.0, "zebrafish data1", "0:50 1:50", "A:1065764997;C:896043530;G:867105444;T:1071973870;N:139159", 50, 50, null, null, 1065764997, 896043530, 867105444, 1071973870, 139159, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.95204, 0.94561, 0.11416, 0.11357, 0.68235, 0.68387, 0.47537, 0.47688, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36587, "SRR1562529", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 3298508150.0, 34528793.0, "zebrafish data2", "0:50 1:50", "A:870578872;C:780299206;G:764413584;T:883098619;N:117869", 50, 50, null, null, 870578872, 780299206, 764413584, 883098619, 117869, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.96195, 0.9525, 0.05344, 0.0528, 0.77285, 0.7737, 0.44453, 0.43789, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36588, "SRR1562530", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 5033866800.0, 52047991.0, "zebrafish data6", "0:50 1:50", "A:1318991279;C:1193979085;G:1179037925;T:1341674073;N:184438", 50, 50, null, null, 1318991279, 1193979085, 1179037925, 1341674073, 184438, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.97568, 0.97028, 0.03448, 0.03488, 0.88767, 0.88785, 0.17745, 0.18337, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36589, "SRR1562531", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 4394828000.0, 45714707.0, "zebrafish data3", "0:50 1:50", "A:1146792341;C:1067826128;G:1033443384;T:1146608253;N:157894", 50, 50, null, null, 1146792341, 1067826128, 1033443384, 1146608253, 157894, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.96496, 0.95999, 0.03952, 0.03946, 0.78571, 0.78518, 0.51359, 0.49202, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36590, "SRR1562532", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 3637203400.0, 38182310.0, "zebrafish data4", "0:50 1:50", "A:956604323;C:863740756;G:843429871;T:973297634;N:130816", 50, 50, null, null, 956604323, 863740756, 843429871, 973297634, 130816, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.95377, 0.94653, 0.0656, 0.06507, 0.72448, 0.72541, 0.4157, 0.41707, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36591, "SRR1562533", "SRX204106", "SRS373224", "SRP017135", "PRJNA179237", "Danio rerio strain:SAT Transcriptome or Gene expression", "PRJNA179237", "Other", "Transcriptomic analysis of zebrafish was carried out with the aim of refining genome annotation using proteogenomic strategy. RNA seq analysis of six tissues liver  muscle  eye  brain  intestine pancreas and testes was carried out along with proteomic analysis of 10 organs.", null, null, "Zebrafish transcriptomic profile for Liver  spleen  Testes  Eye  Muscle  Intestine Pancreas", "Zebrafish trancriptome for protegenomic analysis", "zebrafish IOB JHU transcriptome", null, null, null, null, null, null, null, null, null, null, "Zebrafish transcriptome profiling for proteogenomic analysis", "JHU IOB zebrafish RNA Seq", "1", "SRR1562528 belongs to the eye tissue  SRR1562529 belongs to the intestine and pancreas tissue SRR1562530 to the liver tissue SRR1562531 belongs to the muscle tissue SRR1562532 belongs to the spleen tissue SRR1562533 belongs to the testis issue.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiScanSQ", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP017135", null, null, null, null, 4185424200.0, 44832788.0, "zebrafish data5", "0:50 1:50", "A:1143949920;C:959926497;G:921201865;T:1160194111;N:151807", 50, 50, null, null, 1143949920, 959926497, 921201865, 1160194111, 151807, "SRX204106", "SRS373224", "SRA060234", "Johns Hopkins University|Pandey Lab", "Johns Hopkins University", 2, 0.95163, 0.94301, 0.12015, 0.11974, 0.64396, 0.64514, 0.49698, 0.49883, 50, 50, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-system"], [36739, "SRR867022", "SRX286270", "SRS420566", "SRP022549", "PRJNA202401", "Danio rerio Transcriptome or Gene expression", "PRJNA202401", "Other", "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.", null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish", "General Sample for Danio rerio", "ICH", null, "strain:wild type", null, null, null, null, null, null, null, null, "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.", null, null, "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", null, null, "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, null, null, null, null, null, null, null, null, "SRX286270", "SRS420566", "SRA075737", "BAYGEN|NGSP", "BAYGEN", 1, 0.59289, null, 0.09435, null, 0.92669, null, 0.7658, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "3prime", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2013-05-23", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [36740, "SRR867023", "SRX286271", "SRS420566", "SRP022549", "PRJNA202401", "Danio rerio Transcriptome or Gene expression", "PRJNA202401", "Other", "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish.", null, null, "Full transcriptome analysis of early dorsoventral DV patterning in zebrafish", "General Sample for Danio rerio", "ICH", null, "strain:wild type", null, null, null, null, null, null, null, null, "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.", null, null, "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", null, null, "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, null, null, null, null, null, null, null, null, "SRX286271", "SRS420566", "SRA075737", "BAYGEN|NGSP", "BAYGEN", 1, 0.42474, null, 0.06136, null, 0.93434, null, 0.75757, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "3prime", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2013-05-23", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [41381, "SRR4375307", "SRX2226800", "SRS1732678", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B1", "resa AG01072", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B1", "AG01072.1", "AG01072.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01072.1_R1.fastq.gz AG01072.1_R2.fastq.gz", "fastq fastq", 756436968.0, 4976559.0, "AG01072.1 R2.fastq.gz", "0:76 1:76", "A:277813562;C:101592220;G:103435859;T:273576694;N:18633", 76, 76, null, null, 277813562, 101592220, 103435859, 273576694, 18633, "SRX2226800", "SRS1732678", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.00777, 0.00795, 0.00043, 0.00056, 0.99344, 0.99389, 0.43869, 0.43095, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41397, "SRR4375099", "SRX2226671", "SRS1732680", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B3", "resa AG01074", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B3", "AG01074.2", "AG01074.2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01074.2_R1.fastq.gz AG01074.2_R2.fastq.gz", "fastq fastq", 1411678568.0, 9287359.0, "AG01074.2 R1.fastq.gz", "0:76 1:76", "A:518452828;C:189515599;G:191777773;T:511511925;N:420443", 76, 76, null, null, 518452828, 189515599, 191777773, 511511925, 420443, "SRX2226671", "SRS1732680", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.00745, 0.00729, 0.00047, 0.00045, 0.99405, 0.99411, 0.43814, 0.47981, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41398, "SRR4375098", "SRX2226670", "SRS1732680", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B3", "resa AG01074", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B3", "AG01074.1", "AG01074.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01074.1_R1.fastq.gz AG01074.1_R2.fastq.gz", "fastq fastq", 867077312.0, 5704456.0, "AG01074.1 R1.fastq.gz", "0:76 1:76", "A:318238609;C:116633576;G:118737324;T:313446459;N:21344", 76, 76, null, null, 318238609, 116633576, 118737324, 313446459, 21344, "SRX2226670", "SRS1732680", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.00791, 0.00753, 0.00052, 0.00054, 0.99395, 0.99381, 0.45038, 0.44477, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41399, "SRR4375097", "SRX2226669", "SRS1732679", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B2", "resa AG01073", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B2", "AG01073.2", "AG01073.2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01073.2_R1.fastq.gz AG01073.2_R2.fastq.gz", "fastq fastq", 1170921968.0, 7703434.0, "AG01073.2 R1.fastq.gz", "0:76 1:76", "A:430252673;C:156958676;G:158824982;T:424542052;N:343585", 76, 76, null, null, 430252673, 156958676, 158824982, 424542052, 343585, "SRX2226669", "SRS1732679", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.00759, 0.00753, 0.00044, 0.00046, 0.99389, 0.99375, 0.48023, 0.49305, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41400, "SRR4375096", "SRX2226668", "SRS1732679", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B2", "resa AG01073", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B2", "AG01073.1", "AG01073.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01073.1_R1.fastq.gz AG01073.1_R2.fastq.gz", "fastq fastq", 650729936.0, 4281118.0, "AG01073.1 R1.fastq.gz", "0:76 1:76", "A:238957997;C:87418913;G:88996057;T:235340339;N:16630", 76, 76, null, null, 238957997, 87418913, 88996057, 235340339, 16630, "SRX2226668", "SRS1732679", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.00771, 0.00754, 0.00052, 0.00049, 0.99403, 0.9936, 0.46484, 0.42136, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41401, "SRR4375095", "SRX2226667", "SRS1732678", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Mut 64c B1", "resa AG01072", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr HSO3|molecule:RNA|selection:pA|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Mut 64c B1", "AG01072.2", "AG01072.2", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01072.2_R1.fastq.gz AG01072.2_R2.fastq.gz", "fastq fastq", 1293717904.0, 8511302.0, "AG01072.2 R1.fastq.gz", "0:76 1:76", "A:475476006;C:173352933;G:175448573;T:469059516;N:380876", 76, 76, null, null, 475476006, 173352933, 175448573, 469059516, 380876, "SRX2226667", "SRS1732678", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.0072, 0.0071, 0.00042, 0.00038, 0.99397, 0.99385, 0.4403, 0.43351, 76, 76, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41403, "SRR4375093", "SRX2226665", "SRS1732676", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   Needle r2", "resa AG00580", null, "strain:TU/AB|age:not applicable|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|condition:needle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   Needle r2", "AG00580.1", "AG00580.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG00580.1_R1.fastq.gz AG00580.1_R2.fastq.gz", "fastq fastq", 536691936.0, 3530868.0, "AG00580.1 R1.fastq.gz", "0:76 1:76", "A:162711942;C:106417027;G:106484569;T:160130705;N:947693", 76, 76, null, null, 162711942, 106417027, 106484569, 160130705, 947693, "SRX2226665", "SRS1732676", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.85835, 0.85877, 0.03686, 0.03615, 0.96818, 0.96895, 0.47111, 0.47948, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-12-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41827, "SRR5251446", "SRX2557171", "SRS1974564", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR139 B1", "nicoli mutmir AG01645", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR139 B1", "AG01645.1", "AG01645.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01645.1_R1.fastq.gz", "fastq", 1574284140.0, 20714265.0, "AG01645.1 R1.fastq.gz", "0:76", "A:485471345;C:270854124;G:374164721;T:443766613;N:27337", 76, null, null, null, 485471345, 270854124, 374164721, 443766613, 27337, "SRX2557171", "SRS1974564", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.82142, null, 0.14068, null, 0.8002, null, 0.5444, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-27", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41828, "SRR5251445", "SRX2557170", "SRS1974563", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR139 B2", "nicoli mutmir AG01646", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR139 B2", "AG01646.1", "AG01646.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01646.1_R1.fastq.gz", "fastq", 1484740104.0, 19536054.0, "AG01646.1 R1.fastq.gz", "0:76", "A:453388316;C:246477203;G:365031959;T:419816346;N:26280", 76, null, null, null, 453388316, 246477203, 365031959, 419816346, 26280, "SRX2557170", "SRS1974563", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.82649, null, 0.1897, null, 0.79862, null, 0.52759, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41829, "SRR5251444", "SRX2557169", "SRS1974562", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR139 B3", "nicoli mutmir AG01647", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR139 B3", "AG01647.1", "AG01647.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01647.1_R1.fastq.gz", "fastq", 881298660.0, 11596035.0, "AG01647.1 R1.fastq.gz", "0:76", "A:270675838;C:160127586;G:228157662;T:222301246;N:36328", 76, null, null, null, 270675838, 160127586, 228157662, 222301246, 36328, "SRX2557169", "SRS1974562", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76133, null, 0.15034, null, 0.83341, null, 0.56596, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41830, "SRR5251443", "SRX2557168", "SRS1974561", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B1", "nicoli mutmir AG01648", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B1", "AG01648.1", "AG01648.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01648.1_R1.fastq.gz", "fastq", 637896880.0, 8393380.0, "AG01648.1 R1.fastq.gz", "0:76", "A:192829278;C:112701153;G:153321271;T:179019095;N:26083", 76, null, null, null, 192829278, 112701153, 153321271, 179019095, 26083, "SRX2557168", "SRS1974561", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75971, null, 0.1181, null, 0.82171, null, 0.56797, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41831, "SRR5251442", "SRX2557167", "SRS1974560", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B2", "nicoli mutmir AG01649", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B2", "AG01649.1", "AG01649.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01649.1_R1.fastq.gz", "fastq", 849868328.0, 11182478.0, "AG01649.1 R1.fastq.gz", "0:76", "A:258225905;C:148467172;G:205165181;T:237974100;N:35970", 76, null, null, null, 258225905, 148467172, 205165181, 237974100, 35970, "SRX2557167", "SRS1974560", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75096, null, 0.14506, null, 0.81507, null, 0.5545, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41832, "SRR5251441", "SRX2557166", "SRS1974559", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B3", "nicoli mutmir AG01650", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B3", "AG01650.1", "AG01650.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01650.1_R1.fastq.gz", "fastq", 998464668.0, 13137693.0, "AG01650.1 R1.fastq.gz", "0:76", "A:311526420;C:176545041;G:251852786;T:258497630;N:42791", 76, null, null, null, 311526420, 176545041, 251852786, 258497630, 42791, "SRX2557166", "SRS1974559", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76479, null, 0.11192, null, 0.82674, null, 0.54621, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41833, "SRR5251440", "SRX2557165", "SRS1974558", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B1", "nicoli mutmir AG01651", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B1", "AG01651.1", "AG01651.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01651.1_R1.fastq.gz", "fastq", 570492252.0, 7506477.0, "AG01651.1 R1.fastq.gz", "0:76", "A:162512811;C:104071716;G:135730697;T:168149427;N:27601", 76, null, null, null, 162512811, 104071716, 135730697, 168149427, 27601, "SRX2557165", "SRS1974558", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.73988, null, 0.10157, null, 0.86647, null, 0.54252, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41834, "SRR5251439", "SRX2557164", "SRS1974557", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B2", "nicoli mutmir AG01652", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B2", "AG01652.1", "AG01652.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01652.1_R1.fastq.gz", "fastq", 1072886148.0, 14116923.0, "AG01652.1 R1.fastq.gz", "0:76", "A:338399596;C:192703439;G:242960887;T:298769761;N:52465", 76, null, null, null, 338399596, 192703439, 242960887, 298769761, 52465, "SRX2557164", "SRS1974557", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76456, null, 0.11024, null, 0.89197, null, 0.59214, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41835, "SRR5251438", "SRX2557163", "SRS1974556", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B3", "nicoli mutmir AG01653", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B3", "AG01653.1", "AG01653.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01653.1_R1.fastq.gz", "fastq", 1016374144.0, 13373344.0, "AG01653.1 R1.fastq.gz", "0:76", "A:310958343;C:168702106;G:223420046;T:313241363;N:52286", 76, null, null, null, 310958343, 168702106, 223420046, 313241363, 52286, "SRX2557163", "SRS1974556", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75735, null, 0.12224, null, 0.79756, null, 0.55136, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41836, "SRR5251437", "SRX2557162", "SRS1974555", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B1", "nicoli mutmir AG01654", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B1", "AG01654.1", "AG01654.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01654.1_R1.fastq.gz", "fastq", 782170112.0, 10291712.0, "AG01654.1 R1.fastq.gz", "0:76", "A:238316720;C:132163709;G:179301544;T:232350598;N:37541", 76, null, null, null, 238316720, 132163709, 179301544, 232350598, 37541, "SRX2557162", "SRS1974555", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.7683, null, 0.10712, null, 0.80034, null, 0.55804, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41837, "SRR5251436", "SRX2557161", "SRS1974554", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B2", "nicoli mutmir AG01655", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B2", "AG01655.1", "AG01655.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01655.1_R1.fastq.gz", "fastq", 1053946340.0, 13867715.0, "AG01655.1 R1.fastq.gz", "0:76", "A:318351311;C:191163031;G:240348413;T:304030367;N:53218", 76, null, null, null, 318351311, 191163031, 240348413, 304030367, 53218, "SRX2557161", "SRS1974554", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.77588, null, 0.07983, null, 0.83934, null, 0.56228, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41838, "SRR5251435", "SRX2557160", "SRS1974553", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B3", "nicoli mutmir AG01656", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B3", "AG01656.1", "AG01656.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01656.1_R1.fastq.gz", "fastq", 1182467736.0, 15558786.0, "AG01656.1 R1.fastq.gz", "0:76", "A:344465226;C:204677242;G:269228338;T:364036735;N:60195", 76, null, null, null, 344465226, 204677242, 269228338, 364036735, 60195, "SRX2557160", "SRS1974553", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.78956, null, 0.13495, null, 0.81517, null, 0.56342, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41839, "SRR5251434", "SRX2557159", "SRS1974552", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B1", "nicoli mutmir AG01657", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B1", "AG01657.1", "AG01657.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01657.1_R1.fastq.gz", "fastq", 536336712.0, 7057062.0, "AG01657.1 R1.fastq.gz", "0:76", "A:158301607;C:93070120;G:121382262;T:163555487;N:27236", 76, null, null, null, 158301607, 93070120, 121382262, 163555487, 27236, "SRX2557159", "SRS1974552", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76425, null, 0.1278, null, 0.84222, null, 0.55305, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41840, "SRR5251433", "SRX2557158", "SRS1974551", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B2", "nicoli mutmir AG01658", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B2", "AG01658.1", "AG01658.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01658.1_R1.fastq.gz", "fastq", 798581856.0, 10507656.0, "AG01658.1 R1.fastq.gz", "0:76", "A:241352089;C:134327379;G:183394123;T:239469845;N:38420", 76, null, null, null, 241352089, 134327379, 183394123, 239469845, 38420, "SRX2557158", "SRS1974551", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76221, null, 0.13398, null, 0.82459, null, 0.55228, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41841, "SRR5251432", "SRX2557157", "SRS1974550", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B3", "nicoli mutmir AG01659", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B3", "AG01659.1", "AG01659.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01659.1_R1.fastq.gz", "fastq", 1093998948.0, 14394723.0, "AG01659.1 R1.fastq.gz", "0:76", "A:330741822;C:186325335;G:249557623;T:327320449;N:53719", 76, null, null, null, 330741822, 186325335, 249557623, 327320449, 53719, "SRX2557157", "SRS1974550", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.77108, null, 0.14674, null, 0.80955, null, 0.55819, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41842, "SRR5251431", "SRX2557156", "SRS1974549", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B1", "nicoli mutmir AG01660", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B1", "AG01660.1", "AG01660.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01660.1_R1.fastq.gz", "fastq", 849905492.0, 11182967.0, "AG01660.1 R1.fastq.gz", "0:76", "A:250953875;C:146191904;G:190040699;T:262674911;N:44103", 76, null, null, null, 250953875, 146191904, 190040699, 262674911, 44103, "SRX2557156", "SRS1974549", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.7687, null, 0.14192, null, 0.82842, null, 0.5344, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41843, "SRR5251430", "SRX2557155", "SRS1974548", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B2", "nicoli mutmir AG01661", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B2", "AG01661.1", "AG01661.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01661.1_R1.fastq.gz", "fastq", 840115400.0, 11054150.0, "AG01661.1 R1.fastq.gz", "0:76", "A:257057495;C:141775085;G:188281166;T:252960590;N:41064", 76, null, null, null, 257057495, 141775085, 188281166, 252960590, 41064, "SRX2557155", "SRS1974548", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.74292, null, 0.10759, null, 0.83615, null, 0.55136, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [42492, "SRR5681431", "SRX2916758", "SRS2282896", "SRP109143", "PRJNA389374", "Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis", "PRJNA389374", "Whole Genome Sequencing", "the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.", null, null, null, null, "15um", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:15um|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "15um zebrafish", "15um zebrafish", "15um zebrafish", "15um zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP109143", null, null, "15um_2.fq.gz 15um_1.fq.gz", "fastq fastq", 4510379400.0, 22551897.0, "15um 2.fq.gz", "0:100 1:100", "A:1183709237;C:1078933188;G:1057042534;T:1190615427;N:79014", 100, 100, null, null, 1183709237, 1078933188, 1057042534, 1190615427, 79014, "SRX2916758", "SRS2282896", "SRA574072", "The Chinese University of HongKong|School of Biomedical Sciences", "The Chinese University of HongKong", 2, 0.95073, 0.95055, 0.0647, 0.06526, 0.67176, 0.67351, 0.46247, 0.46176, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-06-14", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42493, "SRR5681432", "SRX2916757", "SRS2282895", "SRP109143", "PRJNA389374", "Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis", "PRJNA389374", "Whole Genome Sequencing", "the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.", null, null, null, null, "10um", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:10um|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "10um zebrafish", "10um zebrafish", "10um zebrafish", "10um zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP109143", null, null, "10um_1.fq.gz 10um_2.fq.gz", "fastq fastq", 4513300800.0, 22566504.0, "10um 1.fq.gz", "0:100 1:100", "A:1186008993;C:1078123999;G:1056044415;T:1193043558;N:79835", 100, 100, null, null, 1186008993, 1078123999, 1056044415, 1193043558, 79835, "SRX2916757", "SRS2282895", "SRA574072", "The Chinese University of HongKong|School of Biomedical Sciences", "The Chinese University of HongKong", 2, 0.94799, 0.94687, 0.07002, 0.06979, 0.66667, 0.66746, 0.47255, 0.47338, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-06-14", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42494, "SRR5681433", "SRX2916756", "SRS2282894", "SRP109143", "PRJNA389374", "Functional role of Eriocalyxin B in zebrafish revealed by transcriptome analysis", "PRJNA389374", "Whole Genome Sequencing", "the first study to comprehensively explore the effects of EriB in zebrafish model using a transcriptome analysis approach.", null, null, null, null, "control", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|sex:not determined|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "control zebrafish", "control zebrafish", "control zebrafish", "control zebrafish", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP109143", null, null, "con_1.fq.gz con_2.fq.gz", "fastq fastq", 4514603400.0, 22573017.0, "con 2.fq.gz", "0:100 1:100", "A:1183878943;C:1081336890;G:1058805201;T:1190503424;N:78942", 100, 100, null, null, 1183878943, 1081336890, 1058805201, 1190503424, 78942, "SRX2916756", "SRS2282894", "SRA574072", "The Chinese University of HongKong|School of Biomedical Sciences", "The Chinese University of HongKong", 2, 0.951, 0.95009, 0.0669, 0.06735, 0.6659, 0.66681, 0.46599, 0.46703, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "China", "2017-06-14", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43083, "SRR7264587", "SRX4168710", "SRS3380684", "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.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.4;AG01270.4", "AG01269.4;AG01270.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MYYANXX_JBCX101_016_R1.fastq.gz", "fastq", 3504515800.0, 46112050.0, "C7MYYANXX JBCX101 016 R1.fastq.gz", "0:76", "A:1100987855;C:897481291;G:850509260;T:655386223;N:151171", 76, null, null, null, 1100987855, 897481291, 850509260, 655386223, 151171, "SRX4168710", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00251, null, 0.00024, null, 0.99334, null, 0.49363, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-05", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43084, "SRR7264588", "SRX4168709", "SRS3380684", "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.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.3;AG01270.3", "AG01269.3;AG01270.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVJ7NADXX_JBCX101_016_R1.fastq.gz", "fastq", 1533760484.0, 20181059.0, "HVJ7NADXX JBCX101 016 R1.fastq.gz", "0:76", "A:486730101;C:387546602;G:372319444;T:287072948;N:91389", 76, null, null, null, 486730101, 387546602, 372319444, 287072948, 91389, "SRX4168709", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 4e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43086, "SRR7264590", "SRX4168707", "SRS3380684", "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.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.5;AG01270.5", "AG01269.5;AG01270.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "C7MWLANXX_JBCX101_016_R1.fastq.gz", "fastq", 11187105076.0, 147198751.0, "C7MWLANXX JBCX101 016 R1.fastq.gz", "0:76", "A:3525623658;C:2869684594;G:2708534500;T:2083102664;N:159660", 76, null, null, null, 3525623658, 2869684594, 2708534500, 2083102664, 159660, "SRX4168707", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43089, "SRR7264593", "SRX4168704", "SRS3380684", "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.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.2;AG01270.2", "AG01269.2;AG01270.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HVK53ADXX_JBCX101_016_R1.fastq.gz", "fastq", 4318423208.0, 56821358.0, "HVK53ADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1370691469;C:1101595011;G:1048719303;T:796936406;N:481019", 76, null, null, null, 1370691469, 1101595011, 1048719303, 796936406, 481019, "SRX4168704", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43090, "SRR7264594", "SRX4168703", "SRS3380684", "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.", null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "Raw multiplex: dmsseq AG01269;dmsseq AG01270", null, "strain:TU/AB|age:2|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2;1|barcode:AGAG;CACA|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Raw multiplex: DMS Seq   IVT 64c B2;DMS Seq   IVT 64c B1", "AG01269.1;AG01270.1", "AG01269.1;AG01270.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "HMHGVADXX_JBCX101_016_R1.fastq.gz", "fastq", 3247405520.0, 42729020.0, "HMHGVADXX JBCX101 016 R1.fastq.gz", "0:76", "A:1030573532;C:829398246;G:789085434;T:598013908;N:334400", 76, null, null, null, 1030573532, 829398246, 789085434, 598013908, 334400, "SRX4168703", "SRS3380684", "SRA715414", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43095, "SRR5893054", "SRX3058791", "SRS2404524", "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.", null, null, null, "miniRESA   2h pA RNA B1", "miniresa AG01710", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B1", "AG01710.1", "AG01710.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01710.1_R1.fastq.gz", "fastq", 236178588.0, 3107613.0, "AG01710.1 R1.fastq.gz", "0:76", "A:63902747;C:43772893;G:46507615;T:81990822;N:4511", 76, null, null, null, 63902747, 43772893, 46507615, 81990822, 4511, "SRX3058791", "SRS2404524", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.92111, null, 4e-05, null, 0.99799, null, 0.56316, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43096, "SRR5893055", "SRX3058790", "SRS2404526", "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.", null, null, null, "miniRESA   2h pA RNA B2", "miniresa AG01711", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B2", "AG01711.1", "AG01711.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01711.1_R1.fastq.gz", "fastq", 226089360.0, 2974860.0, "AG01711.1 R1.fastq.gz", "0:76", "A:61341697;C:41846683;G:44622362;T:78273216;N:5402", 76, null, null, null, 61341697, 41846683, 44622362, 78273216, 5402, "SRX3058790", "SRS2404526", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.91845, null, 1e-05, null, 0.99797, null, 0.60522, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43153, "SRR5893120", "SRX3058725", "SRS2404546", "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.", null, null, null, "DMS Seq   IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B2", "AG01269.2", "AG01269.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.2_R1.fastq.gz", "fastq", 615648941.0, 27257391.0, "AG01269.2 R1.fastq.gz", "0:22.59 1:0", "A:163885634;C:143593857;G:157437520;T:150675530;N:56400", 22, 0, null, null, 163885634, 143593857, 157437520, 150675530, 56400, "SRX3058725", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6277, null, 0.07639, null, 0.78236, null, 0.60487, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43154, "SRR5893121", "SRX3058724", "SRS2404546", "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.", null, null, null, "DMS Seq   IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B2", "AG01269.1", "AG01269.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.1_R1.fastq.gz", "fastq", 461341500.0, 20486790.0, "AG01269.1 R1.fastq.gz", "0:22.52 1:0", "A:122338299;C:107915972;G:118163678;T:112917569;N:5982", 22, 0, null, null, 122338299, 107915972, 118163678, 112917569, 5982, "SRX3058724", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62415, null, 0.07628, null, 0.78133, null, 0.60032, null, 19, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43159, "SRR8782100", "SRX3058719", "SRS2404551", "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.", null, null, null, "miniRESA   2h pA RNA B4", "miniresa AG01728", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B4", "AG01728.1", "AG01728.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893126_replace_R1.fastq.gz", "fastq", 156537732.0, 2059707.0, "SRR5893126 replace R1.fastq.gz", "0:76", "A:42070748;C:29088642;G:31333987;T:54029008;N:15347", 76, null, null, null, 42070748, 29088642, 31333987, 54029008, 15347, "SRX3058719", "SRS2404551", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94152, null, 0.0, null, 0.99797, null, 0.61884, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43160, "SRR8782101", "SRX3058718", "SRS2404553", "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.", null, null, null, "miniRESA   2h pA RNA B3", "miniresa AG01727", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B3", "AG01727.1", "AG01727.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893127_replace_R1.fastq.gz", "fastq", 150519748.0, 1980523.0, "SRR5893127 replace R1.fastq.gz", "0:76", "A:40089061;C:28406150;G:30480481;T:51528116;N:15940", 76, null, null, null, 40089061, 28406150, 30480481, 51528116, 15940, "SRX3058718", "SRS2404553", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.94224, null, 1e-05, null, 0.99793, null, 0.60622, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43162, "SRR8782104", "SRX3058716", "SRS2404554", "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.", null, null, null, "miniRESA   2h pA RNA B5", "miniresa AG01729", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:25|replicate:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miniRESA   2h pA RNA B5", "AG01729.1", "AG01729.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "SRR5893129_replace_R1.fastq.gz", "fastq", 164152628.0, 2159903.0, "SRR5893129 replace R1.fastq.gz", "0:76", "A:44289887;C:30688789;G:32985693;T:56172026;N:16233", 76, null, null, null, 44289887, 30688789, 32985693, 56172026, 16233, "SRX3058716", "SRS2404554", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.9284, null, 1e-05, null, 0.9976, null, 0.61504, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43164, "SRR5893131", "SRX3058714", "SRS2404556", "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.", null, null, null, "DMS Seq   IVT 64c B1", "dmsseq AG01270", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B1", "AG01270.4", "AG01270.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01270.4_R1.fastq.gz", "fastq", 369232203.0, 16423574.0, "AG01270.4 R1.fastq.gz", "0:22.48 1:0", "A:96909706;C:86935520;G:96347195;T:89039251;N:531", 22, 0, null, null, 96909706, 86935520, 96347195, 89039251, 531, "SRX3058714", "SRS2404556", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.61992, null, 0.07599, null, 0.78701, null, 0.61408, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43165, "SRR5893132", "SRX3058713", "SRS2404556", "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.", null, null, null, "DMS Seq   IVT 64c B1", "dmsseq AG01270", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B1", "AG01270.5", "AG01270.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01270.5_R1.fastq.gz", "fastq", 1209837988.0, 53770802.0, "AG01270.5 R1.fastq.gz", "0:22.50 1:0", "A:315203598;C:286991445;G:317405494;T:290233476;N:3975", 22, 0, null, null, 315203598, 286991445, 317405494, 290233476, 3975, "SRX3058713", "SRS2404556", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.628, null, 0.07601, null, 0.78675, null, 0.61598, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43166, "SRR5893133", "SRX3058712", "SRS2404556", "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.", null, null, null, "DMS Seq   IVT 64c B1", "dmsseq AG01270", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B1", "AG01270.2", "AG01270.2", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01270.2_R1.fastq.gz", "fastq", 475556869.0, 21124005.0, "AG01270.2 R1.fastq.gz", "0:22.51 1:0", "A:125248500;C:112069047;G:123791782;T:114403721;N:43819", 22, 0, null, null, 125248500, 112069047, 123791782, 114403721, 43819, "SRX3058712", "SRS2404556", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62492, null, 0.07783, null, 0.78451, null, 0.5998, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43167, "SRR5893134", "SRX3058711", "SRS2404556", "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.", null, null, null, "DMS Seq   IVT 64c B1", "dmsseq AG01270", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B1", "AG01270.3", "AG01270.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01270.3_R1.fastq.gz", "fastq", 161875687.0, 7179709.0, "AG01270.3 R1.fastq.gz", "0:22.55 1:0", "A:42971355;C:37785152;G:42094982;T:39023778;N:420", 22, 0, null, null, 42971355, 37785152, 42094982, 39023778, 420, "SRX3058711", "SRS2404556", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62849, null, 0.07622, null, 0.78307, null, 0.60361, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43168, "SRR5893135", "SRX3058710", "SRS2404546", "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.", null, null, null, "DMS Seq   IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B2", "AG01269.5", "AG01269.5", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.5_R1.fastq.gz", "fastq", 1563607961.0, 69286414.0, "AG01269.5 R1.fastq.gz", "0:22.57 1:0", "A:411693836;C:367369547;G:402702896;T:381836642;N:5040", 22, 0, null, null, 411693836, 367369547, 402702896, 381836642, 5040, "SRX3058710", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62646, null, 0.07519, null, 0.78332, null, 0.60197, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43169, "SRR5893136", "SRX3058709", "SRS2404556", "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.", null, null, null, "DMS Seq   IVT 64c B1", "dmsseq AG01270", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B1", "AG01270.1", "AG01270.1", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01270.1_R1.fastq.gz", "fastq", 355558938.0, 15838601.0, "AG01270.1 R1.fastq.gz", "0:22.45 1:0", "A:93238299;C:84024450;G:92763663;T:85527926;N:4600", 22, 0, null, null, 93238299, 84024450, 92763663, 85527926, 4600, "SRX3058709", "SRS2404556", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.62041, null, 0.07796, null, 0.78526, null, 0.60168, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43170, "SRR5893137", "SRX3058708", "SRS2404546", "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.", null, null, null, "DMS Seq   IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B2", "AG01269.3", "AG01269.3", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.3_R1.fastq.gz", "fastq", 212697329.0, 9397171.0, "AG01269.3 R1.fastq.gz", "0:22.63 1:0", "A:57025177;C:49118963;G:54415396;T:52137277;N:516", 22, 0, null, null, 57025177, 49118963, 54415396, 52137277, 516, "SRX3058708", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.63192, null, 0.07668, null, 0.77983, null, 0.6006, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43171, "SRR5893138", "SRX3058707", "SRS2404546", "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.", null, null, null, "DMS Seq   IVT 64c B2", "dmsseq AG01269", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:DMS 0.5% in vitro|molecule:RNA|selection:pA|condition:DMS|replicate group:17|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMS Seq   IVT 64c B2", "AG01269.4", "AG01269.4", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP114782", null, null, "AG01269.4_R1.fastq.gz", "fastq", 474396378.0, 21071500.0, "AG01269.4 R1.fastq.gz", "0:22.51 1:0", "A:125988009;C:110649678;G:121336327;T:116421641;N:723", 22, 0, null, null, 125988009, 110649678, 121336327, 116421641, 723, "SRX3058707", "SRS2404546", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.6211, null, 0.07454, null, 0.78612, null, 0.60194, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [46213, "SRR6477201", "SRX3567063", "SRS2838995", "SRP129892", "PRJNA430431", "RES complex is associated with intron definition and required for zebrafish early embryogenesis", "PRJNA430431", "Other", "Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.", null, null, null, "RNAseq RES complex   rbmx2 SIB 48h", "RNAseq RES complex   rbmx2 SIB 48h AG01558", null, "strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:4|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq RES complex   rbmx2 SIB 48h", "AG01558.1", "AG01558.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP129892", null, null, "AG01558.1_R1.fastq.gz AG01558.1_R2.fastq.gz", "fastq fastq", 9241524912.0, 60799506.0, "AG01558.1 R2.fastq.gz", "0:76 1:76", "A:2590261461;C:2051008707;G:2048932825;T:2547072369;N:4249550", 76, 76, null, null, 2590261461, 2051008707, 2048932825, 2547072369, 4249550, "SRX3567063", "SRS2838995", "SRA647342", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.94691, 0.94614, 0.14206, 0.14368, 0.68093, 0.68004, 0.46358, 0.46633, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-23", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [46214, "SRR6477202", "SRX3567062", "SRS2838994", "SRP129892", "PRJNA430431", "RES complex is associated with intron definition and required for zebrafish early embryogenesis", "PRJNA430431", "Other", "Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.", null, null, null, "RNAseq RES complex   rbmx2 KO 48h", "RNAseq RES complex   rbmx2 KO 48h AG01557", null, "strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:3|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq RES complex   rbmx2 KO 48h", "AG01557.1", "AG01557.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP129892", null, null, "AG01557.1_R1.fastq.gz AG01557.1_R2.fastq.gz", "fastq fastq", 10308923480.0, 67821865.0, "AG01557.1 R2.fastq.gz", "0:76 1:76", "A:2867250947;C:2265018715;G:2268705348;T:2903182748;N:4765722", 76, 76, null, null, 2867250947, 2265018715, 2268705348, 2903182748, 4765722, "SRX3567062", "SRS2838994", "SRA647342", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.93752, 0.94003, 0.18012, 0.18634, 0.68893, 0.6858, 0.46131, 0.46347, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-23", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [46215, "SRR6477203", "SRX3567061", "SRS2838993", "SRP129892", "PRJNA430431", "RES complex is associated with intron definition and required for zebrafish early embryogenesis", "PRJNA430431", "Other", "Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.", null, null, null, "RNAseq RES complex   snip1 SIB 48h", "RNAseq RES complex   snip1 SIB 48h AG01560", null, "strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:+/?|molecule:mRNA|selection:pA|replicate group:6|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq RES complex   snip1 SIB 48h", "AG01560.1", "AG01560.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP129892", null, null, "AG01560.1_R1.fastq.gz AG01560.1_R2.fastq.gz", "fastq fastq", 12336748336.0, 81162818.0, "AG01560.1 R2.fastq.gz", "0:76 1:76", "A:3381905039;C:2782580059;G:2774648248;T:3391983732;N:5631258", 76, 76, null, null, 3381905039, 2782580059, 2774648248, 3391983732, 5631258, "SRX3567061", "SRS2838993", "SRA647342", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.94802, 0.9492, 0.13035, 0.13145, 0.68006, 0.67783, 0.46768, 0.46426, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-23", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [46216, "SRR6477204", "SRX3567060", "SRS2838992", "SRP129892", "PRJNA430431", "RES complex is associated with intron definition and required for zebrafish early embryogenesis", "PRJNA430431", "Other", "Pre mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA binding proteins. The retention and splicing RES complex is formed by three different proteins Bud13p  Pml1p and Snu17p and is involved in splicing in yeast. However  the importance of the RES complex for vertebrate splicing  the intronic features associated with its activity  and its role in development are unknown. In this study  we have generated loss of function mutants for the three components of the RES complex in zebrafish and showed that they are required during early development. The mutants showed a marked neural phenotype with increased cell death in the brain and a decrease in differentiated neurons. Transcriptomic analysis of bud13  snip1 pml1 and rbmx2 snu17 mutants revealed a global defect in intron splicing  with strong mis splicing of a subset of introns. We found these RES dependent introns were short  rich in GC and flanked by GC depleted exons  all of which are features associated with intron definition. Using these features  we developed and validated a predictive model that classifies RES dependent introns. Altogether  our study uncovers the essential role of the RES complex during vertebrate development and provides new insights into its function during splicing.", null, null, null, "RNAseq RES complex   snip1 KO 48h", "RNAseq RES complex   snip1 KO 48h AG01559", null, "strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype: / |molecule:mRNA|selection:pA|replicate group:5|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq RES complex   snip1 KO 48h", "AG01559.1", "AG01559.1", "mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP129892", null, null, "AG01559.1_R1.fastq.gz AG01559.1_R2.fastq.gz", "fastq fastq", 11252234568.0, 74027859.0, "AG01559.1 R1.fastq.gz", "0:76 1:76", "A:3167425566;C:2465030272;G:2448402147;T:3166105639;N:5270944", 76, 76, null, null, 3167425566, 2465030272, 2448402147, 3166105639, 5270944, "SRX3567060", "SRS2838992", "SRA647342", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.93557, 0.9354, 0.19378, 0.19524, 0.69075, 0.6943, 0.46751, 0.47134, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-23", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "mRNA seq   4h trip R0", "mRNA seq   4h trip R0 AGN001745", null, "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", null, null, null, null, null, null, null, null, "mRNA seq   4h trip R0", "AGR002401", "AGR002401", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP184786", null, null, "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, null, null, null, 189288361, 252171181, 262503967, 220509369, 21750, "SRX5354345", "SRS4345563", "SRA847217", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.69029, null, 0.07606, null, 0.77516, null, 0.52854, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-06-12", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51334, "SRR8784145", "SRX5574146", "SRS4536707", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h a Am r2 B1", "RESA   WT 6h a Am r2 B1 AGN000583", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|sample ref:AGS000533|replicate ref:AGN000583|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h a Am r2 B1", "AGR000772", "AGR000772", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000772_R1.fastq.gz AGR000772_R2.fastq.gz", "fastq fastq", 858051704.0, 5645077.0, "AGR000772 R1.fastq.gz", "0:76 1:76", "A:260528161;C:169740216;G:169821501;T:256446553;N:1515273", 76, 76, null, null, 260528161, 169740216, 169821501, 256446553, 1515273, "SRX5574146", "SRS4536707", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85086, 0.85133, 0.03656, 0.0362, 0.96861, 0.96917, 0.47155, 0.47528, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51336, "SRR8784147", "SRX5574144", "SRS4536704", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT TinyLNA430 6h DL B2", "RESA   WT TinyLNA430 6h DL B2 AGN000468", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430|molecule:RNA|sample ref:AGS000445|replicate ref:AGN000468|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT TinyLNA430 6h DL B2", "AGR000602", "AGR000602", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000602_R1.fastq.gz", "fastq", 2627525732.0, 34572707.0, "AGR000602 R1.fastq.gz", "0:76", "A:750015324;C:666424084;G:623763820;T:586999539;N:322965", 76, null, null, null, 750015324, 666424084, 623763820, 586999539, 322965, "SRX5574144", "SRS4536704", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.87853, null, 0.06924, null, 0.78255, null, 0.55641, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51337, "SRR8784148", "SRX5574143", "SRS4536697", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT TinyLNA430 6h DL B1", "RESA   WT TinyLNA430 6h DL B1 AGN000467", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430|molecule:RNA|sample ref:AGS000445|replicate ref:AGN000467|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT TinyLNA430 6h DL B1", "AGR000601", "AGR000601", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000601_R1.fastq.gz", "fastq", 3663991464.0, 48210414.0, "AGR000601 R1.fastq.gz", "0:76", "A:1047383844;C:920761577;G:959252939;T:736380253;N:212851", 76, null, null, null, 1047383844, 920761577, 959252939, 736380253, 212851, "SRX5574143", "SRS4536697", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00056, null, 0.00017, null, 0.99868, null, 0.34782, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51339, "SRR8784150", "SRX5574141", "SRS4536704", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT TinyLNA430 6h DL B2", "RESA   WT TinyLNA430 6h DL B2 AGN000468", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430|molecule:RNA|sample ref:AGS000445|replicate ref:AGN000468|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT TinyLNA430 6h DL B2", "AGR000603", "AGR000603", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000603_R1.fastq.gz", "fastq", 3393300668.0, 44648693.0, "AGR000603 R1.fastq.gz", "0:76", "A:969581621;C:868752008;G:809775803;T:744990313;N:200923", 76, null, null, null, 969581621, 868752008, 809775803, 744990313, 200923, "SRX5574141", "SRS4536704", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.87891, null, 0.06856, null, 0.78317, null, 0.55832, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51340, "SRR8784151", "SRX5574140", "SRS4536703", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h a Am r2 B2", "RESA   WT 6h a Am r2 B2 AGN000588", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|sample ref:AGS000533|replicate ref:AGN000588|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h a Am r2 B2", "AGR000774", "AGR000774", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000774_R1.fastq.gz AGR000774_R2.fastq.gz", "fastq fastq", 1137810440.0, 7485595.0, "AGR000774 R1.fastq.gz", "0:76 1:76", "A:346292154;C:224190817;G:225113116;T:340741657;N:1472696", 76, 76, null, null, 346292154, 224190817, 225113116, 340741657, 1472696, "SRX5574140", "SRS4536703", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85647, 0.85773, 0.03665, 0.03596, 0.96964, 0.97035, 0.4856, 0.4814, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51341, "SRR8784152", "SRX5574139", "SRS4536703", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h a Am r2 B2", "RESA   WT 6h a Am r2 B2 AGN000588", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|sample ref:AGS000533|replicate ref:AGN000588|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h a Am r2 B2", "AGR000773", "AGR000773", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000773_R1.fastq.gz AGR000773_R2.fastq.gz", "fastq fastq", 339886896.0, 2236098.0, "AGR000773 R1.fastq.gz", "0:76 1:76", "A:103041077;C:67427767;G:67512829;T:101310772;N:594451", 76, 76, null, null, 103041077, 67427767, 67512829, 101310772, 594451, "SRX5574139", "SRS4536703", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.8468, 0.84687, 0.03641, 0.03637, 0.96921, 0.96901, 0.47811, 0.47989, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51354, "SRR8784165", "SRX5574126", "SRS4536688", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B2", "RESA   WT a Am 6h DL B2 AGN000466", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000466|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B2", "AGR000599", "AGR000599", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000599_R1.fastq.gz", "fastq", 598577064.0, 7876014.0, "AGR000599 R1.fastq.gz", "0:76", "A:173027792;C:152514326;G:149669126;T:123341073;N:24747", 76, null, null, null, 173027792, 152514326, 149669126, 123341073, 24747, "SRX5574126", "SRS4536688", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00013, null, 1e-05, null, 0.99963, null, 0.52631, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51355, "SRR8784166", "SRX5574125", "SRS4536697", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT TinyLNA430 6h DL B1", "RESA   WT TinyLNA430 6h DL B1 AGN000467", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection tinyLNA miR 430|molecule:RNA|sample ref:AGS000445|replicate ref:AGN000467|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT TinyLNA430 6h DL B1", "AGR000600", "AGR000600", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000600_R1.fastq.gz", "fastq", 2926686508.0, 38509033.0, "AGR000600 R1.fastq.gz", "0:76", "A:834684269;C:728545827;G:762223876;T:600884916;N:347620", 76, null, null, null, 834684269, 728545827, 762223876, 600884916, 347620, "SRX5574125", "SRS4536697", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00012, null, 1e-05, null, 0.99969, null, 0.6, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51356, "SRR8784167", "SRX5574124", "SRS4536696", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h L430 r2 B3", "RESA   WT 6h L430 r2 B3 AGN000593", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|sample ref:AGS000534|replicate ref:AGN000593|replicate order:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h L430 r2 B3", "AGR000779", "AGR000779", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000779_R1.fastq.gz AGR000779_R2.fastq.gz", "fastq fastq", 889245296.0, 5850298.0, "AGR000779 R1.fastq.gz", "0:76 1:76", "A:272234472;C:173681747;G:173883274;T:267900144;N:1545659", 76, 76, null, null, 272234472, 173681747, 173883274, 267900144, 1545659, "SRX5574124", "SRS4536696", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.84547, 0.84612, 0.03639, 0.03635, 0.96944, 0.97039, 0.48497, 0.48773, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51358, "SRR8784169", "SRX5574122", "SRS4536694", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h L430 r2 B2", "RESA   WT 6h L430 r2 B2 AGN000589", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|sample ref:AGS000534|replicate ref:AGN000589|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h L430 r2 B2", "AGR000777", "AGR000777", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000777_R2.fastq.gz AGR000777_R1.fastq.gz", "fastq fastq", 196328368.0, 1291634.0, "AGR000777 R1.fastq.gz", "0:76 1:76", "A:59795542;C:38713329;G:38666257;T:58817928;N:335312", 76, 76, null, null, 59795542, 38713329, 38666257, 58817928, 335312, "SRX5574122", "SRS4536694", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.84756, 0.84807, 0.03654, 0.03624, 0.9694, 0.96934, 0.46519, 0.47071, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51359, "SRR8784170", "SRX5574121", "SRS4536694", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h L430 r2 B2", "RESA   WT 6h L430 r2 B2 AGN000589", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|sample ref:AGS000534|replicate ref:AGN000589|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h L430 r2 B2", "AGR000778", "AGR000778", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000778_R1.fastq.gz AGR000778_R2.fastq.gz", "fastq fastq", 533214328.0, 3507989.0, "AGR000778 R1.fastq.gz", "0:76 1:76", "A:162908369;C:104425656;G:104787994;T:160373088;N:719221", 76, 76, null, null, 162908369, 104425656, 104787994, 160373088, 719221, "SRX5574121", "SRS4536694", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.85621, 0.85778, 0.03697, 0.03641, 0.96988, 0.96968, 0.46864, 0.47413, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51360, "SRR8784171", "SRX5574120", "SRS4536693", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h a Am r2 B3", "RESA   WT 6h a Am r2 B3 AGN000592", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr alpha am|molecule:RNA|sample ref:AGS000533|replicate ref:AGN000592|replicate order:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h a Am r2 B3", "AGR000775", "AGR000775", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000775_R1.fastq.gz AGR000775_R2.fastq.gz", "fastq fastq", 1104549952.0, 7266776.0, "AGR000775 R1.fastq.gz", "0:76 1:76", "A:335891429;C:218153618;G:218325553;T:330250768;N:1928584", 76, 76, null, null, 335891429, 218153618, 218325553, 330250768, 1928584, "SRX5574120", "SRS4536693", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.84907, 0.85057, 0.03617, 0.03574, 0.96944, 0.96944, 0.48591, 0.48735, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51361, "SRR8784172", "SRX5574119", "SRS4536692", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT 6h L430 r2 B1", "RESA   WT 6h L430 r2 B1 AGN000584", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:500utr tinyLNA miR 430|molecule:RNA|sample ref:AGS000534|replicate ref:AGN000584|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT 6h L430 r2 B1", "AGR000776", "AGR000776", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000776_R1.fastq.gz AGR000776_R2.fastq.gz", "fastq fastq", 631123912.0, 4152131.0, "AGR000776 R1.fastq.gz", "0:76 1:76", "A:192110171;C:124358889;G:124501405;T:189051826;N:1101621", 76, 76, null, null, 192110171, 124358889, 124501405, 189051826, 1101621, "SRX5574119", "SRS4536692", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.84407, 0.84597, 0.03569, 0.0355, 0.96972, 0.96988, 0.47078, 0.47862, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51363, "SRR8784174", "SRX5574117", "SRS4536690", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B1", "RESA   WT a Am 6h DL B1 AGN000465", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000465|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B1", "AGR000593", "AGR000593", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000593_R1.fastq.gz", "fastq", 169214000.0, 2226500.0, "AGR000593 R1.fastq.gz", "0:76", "A:48502801;C:44879333;G:42196735;T:33629068;N:6063", 76, null, null, null, 48502801, 44879333, 42196735, 33629068, 6063, "SRX5574117", "SRS4536690", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.75523, null, 0.05708, null, 0.79868, null, 0.56487, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51364, "SRR8784175", "SRX5574116", "SRS4536690", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B1", "RESA   WT a Am 6h DL B1 AGN000465", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000465|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B1", "AGR000594", "AGR000594", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000594_R1.fastq.gz", "fastq", 2077622488.0, 27337138.0, "AGR000594 R1.fastq.gz", "0:76", "A:611435382;C:538245690;G:522186419;T:402325956;N:3429041", 76, null, null, null, 611435382, 538245690, 522186419, 402325956, 3429041, "SRX5574116", "SRS4536690", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00012, null, 1e-05, null, 0.99965, null, 0.58823, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-03-25", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51365, "SRR8784176", "SRX5574115", "SRS4536690", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B1", "RESA   WT a Am 6h DL B1 AGN000465", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000465|replicate order:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B1", "AGR000592", "AGR000592", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000592_R1.fastq.gz", "fastq", 3782773916.0, 49773341.0, "AGR000592 R1.fastq.gz", "0:76", "A:1114409153;C:956769643;G:933746978;T:777498217;N:349925", 76, null, null, null, 1114409153, 956769643, 933746978, 777498217, 349925, "SRX5574115", "SRS4536690", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.88163, null, 0.07197, null, 0.78376, null, 0.48999, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51366, "SRR8784177", "SRX5574114", "SRS4536688", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B2", "RESA   WT a Am 6h DL B2 AGN000466", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000466|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B2", "AGR000595", "AGR000595", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000595_R1.fastq.gz", "fastq", 3181198120.0, 41857870.0, "AGR000595 R1.fastq.gz", "0:76", "A:916117551;C:764906267;G:794289368;T:705583699;N:301235", 76, null, null, null, 916117551, 764906267, 794289368, 705583699, 301235, "SRX5574114", "SRS4536688", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.0001, null, 1e-05, null, 0.99969, null, 0.53333, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51367, "SRR8784178", "SRX5574113", "SRS4536688", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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 RESA libraries part of the study.", null, null, null, "RESA   WT a Am 6h DL B2", "RESA   WT a Am 6h DL B2 AGN000466", null, "strain:TU/AB|age:6|sex:pooled male and female|tissue:embryo|treatment:transcriptome 6h aAm AGN000129 injection alpha am|molecule:RNA|sample ref:AGS000444|replicate ref:AGN000466|replicate order:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA   WT a Am 6h DL B2", "AGR000596", "AGR000596", "RNA", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP189389", null, null, "AGR000596_R1.fastq.gz", "fastq", 379188776.0, 4989326.0, "AGR000596 R1.fastq.gz", "0:76", "A:110241873;C:94609649;G:95730118;T:78592018;N:15118", 76, null, null, null, 110241873, 94609649, 95730118, 78592018, 15118, "SRX5574113", "SRS4536688", "SRA865803", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 1, 0.00012, null, 0.0, null, 0.99963, null, 0.55555, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-05-31", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [51368, "SRR8784179", "SRX5574112", "SRS4536688", "SRP189389", "PRJNA528980", "Genome wide analysis of three prime UTR sequence elements and proteins regulating mRNA stability during maternal to zygotic transition in zebrafish: RESA", "PRJNA528980", "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. 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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. 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