{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and experiment.library_selection = \"RT-PCR\"", "rows": [[29210, "SRR27489726", "SRX23160983", "SRS20111140", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. 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Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:7|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica A", "Library 7", "Library 7", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 11998643314.0, 39730607.0, "BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008", 151, 151, null, null, 3044270548, 3145201016, 2907229129, 2901344613, 598008, "SRX23160980", "SRS20111142", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01631, 0.00013, 0.00035, 1e-05, 0.99101, 0.99965, 0.40542, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29214, "SRR27489730", "SRX23160979", "SRS20111137", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica A", "MPRA repA fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:6|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica A", "Library 6", "Library 6", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12838157410.0, 42510455.0, "BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610", 151, 151, null, null, 3238698530, 3377705608, 3143460419, 3077655243, 637610, "SRX23160979", "SRS20111137", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01549, 3e-05, 0.00042, 1e-05, 0.99097, 0.99995, 0.42138, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29215, "SRR27489731", "SRX23160978", "SRS20111136", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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Reimao Pinto|genotype:not applicable|growth protocol:not applicable|sample type:IVT mRNA|sample number:50|replicate:unique sample|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "control RNA library", "Library 50", "Library 50", "PCR product was amplified from DNA plasmid pool with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16695252486.0, 55282293.0, "BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301", 151, 151, null, null, 4275447149, 4413405571, 3936523108, 4069049357, 827301, "SRX23160978", "SRS20111136", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02176, 0.00021, 0.00058, 2e-05, 0.99056, 0.99933, 0.41475, 0.48571, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [29216, "SRR27489733", "SRX23160976", "SRS20111134", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:48|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 10hpf replica C", "Library 48", "Library 48", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16074911568.0, 53228184.0, "BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275", 151, 151, null, null, 4029048727, 4167204709, 4036912991, 3840941866, 803275, "SRX23160976", "SRS20111134", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.00795, 0.00021, 0.00019, 2e-05, 0.99263, 0.99935, 0.45247, 0.62857, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29217, "SRR27489734", "SRX23160975", "SRS20111132", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:47|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 10hpf replica C", "Library 47", "Library 47", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16211925948.0, 53681874.0, "BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500", 151, 151, null, null, 4078470905, 4239434649, 4000426230, 3892801664, 792500, "SRX23160975", "SRS20111132", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01232, 0.00028, 0.00027, 5e-05, 0.99166, 0.99926, 0.4522, 0.61904, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29218, "SRR27489735", "SRX23160974", "SRS20111131", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:46|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 10hpf replica C", "Library 46", "Library 46", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 18761117310.0, 62122905.0, "BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979", 151, 151, null, null, 4746221682, 4940258209, 4549993563, 4523714877, 928979, "SRX23160974", "SRS20111131", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01785, 0.0002, 0.00043, 3e-05, 0.9908, 0.99951, 0.45866, 0.6, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29219, "SRR27489736", "SRX23160973", "SRS20111130", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 10hpf replica C", "MPRA repC input 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:45|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 10hpf replica C", "Library 45", "Library 45", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15148053334.0, 50159117.0, "BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975", 151, 151, null, null, 3877492548, 4007711111, 3560735163, 3701356537, 757975, "SRX23160973", "SRS20111130", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02196, 3e-05, 0.00062, 1e-05, 0.98944, 0.99993, 0.4404, 0.66666, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29220, "SRR27489737", "SRX23160972", "SRS20111129", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 6hpf replica C", "MPRA repC fractions 8 9 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:44|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 6hpf replica C", "Library 44", "Library 44", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14506315716.0, 48034158.0, "BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665", 151, 151, null, null, 3655344763, 3770081597, 3599601074, 3480562617, 725665, "SRX23160972", "SRS20111129", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01152, 0.00012, 0.00021, 1e-05, 0.99204, 0.99963, 0.40859, 0.47368, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29221, "SRR27489738", "SRX23160971", "SRS20111128", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 6hpf replica C", "MPRA repC fractions 6 7 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:43|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 6hpf replica C", "Library 43", "Library 43", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 14912162946.0, 49378023.0, "BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615", 151, 151, null, null, 3752402181, 3897191999, 3682100517, 3579734634, 733615, "SRX23160971", "SRS20111128", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01301, 0.0001, 0.00023, 0.0, 0.99131, 0.99963, 0.41128, 0.44444, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29222, "SRR27489739", "SRX23160970", "SRS20111127", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 6hpf replica C", "MPRA repC fractions 4 5 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:42|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 6hpf replica C", "Library 42", "Library 42", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16464627468.0, 54518634.0, "BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276", 151, 151, null, null, 4169088631, 4342123158, 3994621055, 3957976348, 818276, "SRX23160970", "SRS20111127", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01689, 8e-05, 0.00051, 0.0, 0.99107, 0.99973, 0.40071, 0.53846, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29223, "SRR27489740", "SRX23160969", "SRS20111125", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 6hpf replica C", "MPRA repC input 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:41|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 6hpf replica C", "Library 41", "Library 41", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10859083158.0, 35957229.0, "BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057", 151, 151, null, null, 2762807814, 2857106152, 2613305234, 2625327901, 536057, "SRX23160969", "SRS20111125", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01753, 0.0, 0.00047, 0.0, 0.9907, 1.0, 0.40097, null, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29224, "SRR27489741", "SRX23160968", "SRS20111133", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica A", "MPRA repA input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:5|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica A", "Library 5", "Library 5", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13631534966.0, 45137533.0, "BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580", 151, 151, null, null, 3486253250, 3611078376, 3219396920, 3314128840, 677580, "SRX23160968", "SRS20111133", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02225, 2e-05, 0.00066, 0.0, 0.98975, 0.99993, 0.40257, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29225, "SRR27489742", "SRX23160967", "SRS20111126", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 4hpf replica C", "MPRA repC fractions 8 9 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:40|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica C", "Library 40", "Library 40", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16854209582.0, 55808641.0, "BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777", 151, 151, null, null, 4270727222, 4383022813, 4143081915, 4056541855, 835777, "SRX23160967", "SRS20111126", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01329, 0.00015, 0.00029, 2e-05, 0.99141, 0.99953, 0.4263, 0.47826, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29226, "SRR27489743", "SRX23160966", "SRS20111124", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 4hpf replica C", "MPRA repC fractions 6 7 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:39|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica C", "Library 39", "Library 39", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12146174844.0, 40219122.0, "BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143", 151, 151, null, null, 3060215849, 3176615755, 3002666854, 2906066243, 610143, "SRX23160966", "SRS20111124", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01309, 0.0002, 0.00031, 0.0, 0.99164, 0.99939, 0.40018, 0.57142, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29227, "SRR27489744", "SRX23160965", "SRS20111123", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica C", "MPRA repC fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:38|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica C", "Library 38", "Library 38", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14100203330.0, 46689415.0, "BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605", 151, 151, null, null, 3544539088, 3702795841, 3493240125, 3358929671, 698605, "SRX23160965", "SRS20111123", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01368, 0.00016, 0.00037, 0.0, 0.99107, 0.99951, 0.40864, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29228, "SRR27489745", "SRX23160964", "SRS20111120", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica C", "MPRA repC input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:37|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica C", "Library 37", "Library 37", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10925301792.0, 36176496.0, "BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085", 151, 151, null, null, 2802490901, 2878602103, 2592316062, 2651349641, 543085, "SRX23160964", "SRS20111120", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02108, 3e-05, 0.0006, 0.0, 0.98981, 0.99991, 0.42181, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29229, "SRR27489746", "SRX23160963", "SRS20111121", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica C", "MPRA repC fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica C", "Library 36", "Library 36", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13085558528.0, 43329664.0, "BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985", 151, 151, null, null, 3305413622, 3391845548, 3249932870, 3137708503, 657985, "SRX23160963", "SRS20111121", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01098, 8e-05, 0.00025, 0.0, 0.99216, 0.99973, 0.4317, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29230, "SRR27489747", "SRX23160962", "SRS20111119", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica C", "MPRA repC fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica C", "Library 35", "Library 35", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16647721914.0, 55124907.0, "BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108", 151, 151, null, null, 4231542934, 4348688006, 4050131444, 4016534422, 825108, "SRX23160962", "SRS20111119", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01514, 0.00017, 0.00035, 3e-05, 0.99109, 0.99955, 0.4372, 0.30434, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29231, "SRR27489748", "SRX23160961", "SRS20111118", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica C", "MPRA repC fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica C", "Library 34", "Library 34", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15431181052.0, 51096626.0, "BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999", 151, 151, null, null, 3856018869, 4036338306, 3877988553, 3660059325, 775999, "SRX23160961", "SRS20111118", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01114, 8e-05, 0.00028, 0.0, 0.99192, 0.99975, 0.42956, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29232, "SRR27489749", "SRX23160960", "SRS20111117", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica C", "MPRA repC input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica C", "Library 33", "Library 33", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 11771229160.0, 38977580.0, "BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080", 151, 151, null, null, 2999574420, 3115525474, 2806539264, 2849003922, 586080, "SRX23160960", "SRS20111117", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01997, 2e-05, 0.00054, 0.0, 0.99022, 0.99993, 0.41853, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29233, "SRR27489750", "SRX23160959", "SRS20111116", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 10hpf replica B", "MPRA repB fractions 8 9 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:32|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 10hpf replica B", "Library 32", "Library 32", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12683073766.0, 41996933.0, "BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624", 151, 151, null, null, 3165850297, 3286094227, 3205853472, 3024640146, 635624, "SRX23160959", "SRS20111116", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.00973, 0.00093, 0.00036, 0.00015, 0.99265, 0.99819, 0.4701, 0.61111, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29234, "SRR27489751", "SRX23160958", "SRS20111115", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 10hpf replica B", "MPRA repB fractions 6 7 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:31|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 10hpf replica B", "Library 31", "Library 31", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11187950286.0, 37046193.0, "BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502", 151, 151, null, null, 2805602272, 2927866458, 2773076846, 2680845208, 559502, "SRX23160958", "SRS20111115", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01142, 0.0002, 0.00018, 2e-05, 0.99243, 0.99943, 0.45894, 0.54838, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29235, "SRR27489752", "SRX23160957", "SRS20111114", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica A", "MPRA repA fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica A", "Library 4", "Library 4", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12108626278.0, 40094789.0, "BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268", 151, 151, null, null, 3079403604, 3149095123, 2953175005, 2926352278, 600268, "SRX23160957", "SRS20111114", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.014, 5e-05, 0.00032, 0.0, 0.99137, 0.99987, 0.45127, 0.28571, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29236, "SRR27489753", "SRX23160956", "SRS20111113", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 10hpf replica B", "MPRA repB fractions 4 5 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:30|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 10hpf replica B", "Library 30", "Library 30", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 15465851256.0, 51211428.0, "BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024", 151, 151, null, null, 3889753740, 4075740540, 3791174754, 3708409198, 773024, "SRX23160956", "SRS20111113", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01609, 0.00014, 0.0003, 3e-05, 0.99139, 0.99959, 0.4335, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29237, "SRR27489754", "SRX23160955", "SRS20111112", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 10hpf replica B", "MPRA repB input 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:29|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 10hpf replica B", "Library 29", "Library 29", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12592035866.0, 41695483.0, "BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448", 151, 151, null, null, 3220865280, 3326103488, 2978281202, 3066156448, 629448, "SRX23160955", "SRS20111112", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02168, 1e-05, 0.0006, 0.0, 0.98993, 0.99997, 0.41273, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29238, "SRR27489755", "SRX23160954", "SRS20111122", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 6hpf replica B", "MPRA repB fractions 8 9 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:28|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 6hpf replica B", "Library 28", "Library 28", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12606651156.0, 41743878.0, "BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136", 151, 151, null, null, 3184687427, 3283680489, 3107570485, 3030085619, 627136, "SRX23160954", "SRS20111122", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01219, 7e-05, 0.00028, 0.0, 0.99182, 0.99977, 0.42217, 0.45454, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29239, "SRR27489756", "SRX23160953", "SRS20111110", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 6hpf replica B", "MPRA repB fractions 6 7 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:27|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 6hpf replica B", "Library 27", "Library 27", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 13738263880.0, 45490940.0, "BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066", 151, 151, null, null, 3463772316, 3608023656, 3363805269, 3301974573, 688066, "SRX23160953", "SRS20111110", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01443, 0.00014, 0.00028, 1e-05, 0.99117, 0.99957, 0.38916, 0.45833, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29240, "SRR27489757", "SRX23160952", "SRS20111111", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 6hpf replica B", "MPRA repB fractions 4 5 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:26|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 6hpf replica B", "Library 26", "Library 26", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 10624262152.0, 35179676.0, "BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277", 151, 151, null, null, 2680084455, 2804915710, 2592024460, 2546707250, 530277, "SRX23160952", "SRS20111111", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01636, 0.00013, 0.00046, 0.0, 0.99088, 0.99959, 0.39222, 0.40909, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29241, "SRR27489758", "SRX23160951", "SRS20111109", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 6hpf replica B", "MPRA repB input 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:25|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 6hpf replica B", "Library 25", "Library 25", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 10153888998.0, 33622149.0, "BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963", 151, 151, null, null, 2587160061, 2673241688, 2432503358, 2460478928, 504963, "SRX23160951", "SRS20111109", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01911, 2e-05, 0.00061, 0.0, 0.99064, 0.99995, 0.42802, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29242, "SRR27489759", "SRX23160950", "SRS20111107", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 4hpf replica B", "MPRA repB fractions 8 9 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:24|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica B", "Library 24", "Library 24", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11600767978.0, 38413139.0, "BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432", 151, 151, null, null, 2943303855, 3024500200, 2833306086, 2799077405, 580432, "SRX23160950", "SRS20111107", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01371, 0.00013, 0.00031, 1e-05, 0.99143, 0.99955, 0.41912, 0.5909, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29243, "SRR27489760", "SRX23160949", "SRS20111106", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 4hpf replica B", "MPRA repB fractions 6 7 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:23|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 4hpf replica B", "Library 23", "Library 23", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13216553444.0, 43763422.0, "BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534", 151, 151, null, null, 3339016083, 3457419680, 3233764657, 3185687490, 665534, "SRX23160949", "SRS20111106", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01431, 0.00024, 0.00034, 1e-05, 0.99135, 0.99924, 0.41915, 0.45238, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29244, "SRR27489761", "SRX23160948", "SRS20111105", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 4hpf replica B", "MPRA repB fractions 4 5 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:22|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 4hpf replica B", "Library 22", "Library 22", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11938250562.0, 39530631.0, "BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415", 151, 151, null, null, 3040684418, 3144238599, 2873359599, 2879374531, 593415, "SRX23160948", "SRS20111105", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0185, 8e-05, 0.00056, 0.0, 0.9903, 0.99969, 0.4376, 0.4, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29245, "SRR27489762", "SRX23160947", "SRS20111104", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 4hpf replica B", "MPRA repB input 4hpf", null, "strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:21|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 4hpf replica B", "Library 21", "Library 21", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 14482326346.0, 47954723.0, "BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777", 151, 151, null, null, 3697691325, 3838972714, 3432418300, 3512522230, 721777, "SRX23160947", "SRS20111104", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0211, 2e-05, 0.00055, 0.0, 0.9903, 0.99993, 0.42543, 0.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [29246, "SRR27489763", "SRX23160946", "SRS20111108", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica A", "MPRA repA fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica A", "Library 3", "Library 3", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12524202136.0, 41470868.0, "BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842", 151, 151, null, null, 3168466372, 3269998328, 3075956662, 3009160932, 619842, "SRX23160946", "SRS20111108", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01351, 7e-05, 0.00028, 0.0, 0.99168, 0.99977, 0.43472, 0.54545, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29247, "SRR27489764", "SRX23160945", "SRS20111103", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 2hpf replica B", "MPRA repB fractions 8 9 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 2hpf replica B", "Library 20", "Library 20", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12514444214.0, 41438557.0, "BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303", 151, 151, null, null, 3174354240, 3246812350, 3082021359, 3010633962, 622303, "SRX23160945", "SRS20111103", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01121, 0.00016, 0.00027, 1e-05, 0.99204, 0.99953, 0.43533, 0.5, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29248, "SRR27489765", "SRX23160944", "SRS20111102", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 2hpf replica B", "MPRA repB fractions 6 7 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 2hpf replica B", "Library 19", "Library 19", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 16535129670.0, 54752085.0, "BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421", 151, 151, null, null, 4184643114, 4312135767, 4051628900, 3985895468, 826421, "SRX23160944", "SRS20111102", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01416, 0.00017, 0.00031, 1e-05, 0.9917, 0.99941, 0.40732, 0.6, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29249, "SRR27489766", "SRX23160943", "SRS20111101", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica B", "MPRA repB fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica B", "Library 18", "Library 18", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 12692870042.0, 42029371.0, "BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284", 151, 151, null, null, 3179006274, 3325152682, 3173386021, 3014687781, 637284, "SRX23160943", "SRS20111101", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01199, 8e-05, 0.0003, 1e-05, 0.99145, 0.99979, 0.40897, 0.36363, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29250, "SRR27489767", "SRX23160942", "SRS20111100", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica B", "MPRA repB input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica B", "Library 17", "Library 17", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13169436008.0, 43607404.0, "BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755", 151, 151, null, null, 3341908647, 3485072739, 3171200836, 3170595031, 658755, "SRX23160942", "SRS20111100", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01868, 5e-05, 0.0006, 0.0, 0.99038, 0.99983, 0.41955, 0.125, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29251, "SRR27489768", "SRX23160941", "SRS20111099", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 10hpf replica A", "MPRA repA fractions 8 9 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:16|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 10hpf replica A", "Library 16", "Library 16", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13501095730.0, 44705615.0, "BSSE QGF 206651 HGWLYDSX3 3 MPRA repA fractions 8 9 10hpf CGGCGTGA GCGCCTGT S16 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3386778587;C:3499255836;G:3382745292;T:3231634315;N:681700", 151, 151, null, null, 3386778587, 3499255836, 3382745292, 3231634315, 681700, "SRX23160941", "SRS20111099", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.00829, 0.00016, 0.00011, 0.0, 0.99265, 0.99949, 0.49527, 0.48275, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29252, "SRR27489769", "SRX23160940", "SRS20111096", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 10hpf replica A", "MPRA repA fractions 6 7 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:15|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 10hpf replica A", "Library 15", "Library 15", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13046767232.0, 43201216.0, "BSSE QGF 206650 HGWLYDSX3 3 MPRA repA fractions 6 7 10hpf TAATACAG ATATTCAC S15 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3290688159;C:3400409529;G:3214905336;T:3140115501;N:648707", 151, 151, null, null, 3290688159, 3400409529, 3214905336, 3140115501, 648707, "SRX23160940", "SRS20111096", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01093, 0.0001, 0.00011, 0.0, 0.99249, 0.99967, 0.43443, 0.77777, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29253, "SRR27489770", "SRX23160939", "SRS20111097", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 10hpf replica A", "MPRA repA fractions 4 5 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:14|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 10hpf replica A", "Library 14", "Library 14", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 13986764580.0, 46313790.0, "BSSE QGF 206649 HGWLYDSX3 3 MPRA repA fractions 4 5 10hpf AATCCGGA CTACAGTT S14 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3536884918;C:3676313944;G:3410122661;T:3362749616;N:693441", 151, 151, null, null, 3536884918, 3676313944, 3410122661, 3362749616, 693441, "SRX23160939", "SRS20111097", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01503, 7e-05, 0.00035, 0.0, 0.99141, 0.99983, 0.43326, 0.77777, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29254, "SRR27489771", "SRX23160938", "SRS20111095", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 10hpf replica A", "MPRA repA input 10hpf", null, "strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:13|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 10hpf replica A", "Library 13", "Library 13", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 11263507666.0, 37296383.0, "BSSE QGF 206648 HGWLYDSX3 3 MPRA repA input 10hpf GGCTTAAG TCGTGACC S13 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2881851385;C:2968960112;G:2663338223;T:2748794775;N:563171", 151, 151, null, null, 2881851385, 2968960112, 2663338223, 2748794775, 563171, "SRX23160938", "SRS20111095", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.02096, 1e-05, 0.00058, 0.0, 0.99022, 0.99997, 0.43837, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29255, "SRR27489772", "SRX23160937", "SRS20111098", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "HMW fraction 6hpf replica A", "MPRA repA fractions 8 9 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:12|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 6hpf replica A", "Library 12", "Library 12", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 14724761980.0, 48757490.0, "BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179", 151, 151, null, null, 3711442998, 3830334531, 3642299006, 3539948266, 737179, "SRX23160937", "SRS20111098", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01161, 8e-05, 0.0002, 1e-05, 0.99214, 0.99985, 0.4529, 0.3, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29256, "SRR27489773", "SRX23160936", "SRS20111094", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "LMW fraction 6hpf replica A", "MPRA repA fractions 6 7 6hpf", null, "strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:11|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "LMW fraction 6hpf replica A", "Library 11", "Library 11", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16713361312.0, 55342256.0, "BSSE QGF 206646 HGWLYDSX3 3 MPRA repA fractions 6 7 6hpf CCAAGTCT AAGGATGA S11 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4183339886;C:4365661507;G:4181177026;T:3982339731;N:843162", 151, 151, null, null, 4183339886, 4365661507, 4181177026, 3982339731, 843162, "SRX23160936", "SRS20111094", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01132, 0.00011, 0.00024, 0.0, 0.99174, 0.99965, 0.40968, 0.47368, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [29257, "SRR27489774", "SRX23160935", "SRS20111093", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "polysome fraction", "80S fraction 2hpf replica A", "MPRA repA fractions 4 5 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "80S fraction 2hpf replica A", "Library 2", "Library 2", "Total RNA was extracted from polysome fractionated sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 16111078182.0, 53347941.0, "BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034", 151, 151, null, null, 4069536779, 4222816450, 3957789955, 3860129964, 805034, "SRX23160935", "SRS20111093", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01511, 5e-05, 0.00034, 0.0, 0.99135, 0.99985, 0.41564, 0.42857, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [29258, "SRR27489775", "SRX23160934", "SRS20111092", "SRP483112", "PRJNA1056276", "five prime UTR MPRA during early zebrafish embryogenesis", "PRJNA1056276", "Other", "The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.", null, null, "input sample", "Total 2hpf replica A", "MPRA repA input 2hpf", null, "strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Total 2hpf replica A", "Library 1", "Library 1", "Total RNA was extracted from input sample  RT was performed with reporter specific primer  UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.", null, null, "OTHER", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483112", null, null, "BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz", "fastq fastq", 9769305890.0, 32348695.0, "BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485", 151, 151, null, null, 2477269774, 2598109179, 2338444856, 2354997596, 484485, "SRX23160934", "SRS20111092", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.0205, 4e-05, 0.00059, 0.0, 0.99013, 0.99987, 0.41957, 0.33333, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-11", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [30599, "SRR27865238", "SRX23527802", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con MO", "6", "6", "con MO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "con-KDM_1.fq.gz con-KDM_2.fq.gz", "fastq fastq", 7088132100.0, 23627107.0, "con KDM 1.fq.gz", "0:150 1:150", "A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033", 150, 150, null, null, 1893419600, 1649526065, 1662549202, 1882459200, 178033, "SRX23527802", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30600, "SRR27865239", "SRX23527801", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "KDM4C MO", "5", "5", "KDM4C MO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "KDM-MO_1.fq.gz KDM-MO_2.fq.gz", "fastq fastq", 7876840500.0, 26256135.0, "KDM MO 1.fq.gz", "0:150 1:150", "A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469", 150, 150, null, null, 2104173142, 1831662159, 1843980192, 2096831538, 193469, "SRX23527801", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30601, "SRR27865240", "SRX23527800", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ZNF662 MO", "4", "4", "ZNF662 MO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "znf547-MO_1.fq.gz znf547-MO_2.fq.gz", "fastq fastq", 7573815300.0, 25246051.0, "znf547 MO 1.fq.gz", "0:150 1:150", "A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628", 150, 150, null, null, 2014197761, 1766587259, 1782217029, 2010540623, 272628, "SRX23527800", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30602, "SRR27865241", "SRX23527799", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "SEMA5A RNA", "3", "3", "SEMA5A RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "semRNA_1.fq.gz semRNA_2.fq.gz", "fastq fastq", 5575566000.0, 18585220.0, "semRNA 1.fq.gz", "0:150 1:150", "A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165", 150, 150, null, null, 1456001758, 1325628099, 1339796989, 1454076989, 62165, "SRX23527799", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30603, "SRR27865242", "SRX23527798", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "MT ATP6 RNA", "2", "2", "MT ATP6 RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz", "fastq fastq", 5437771200.0, 18125904.0, "ATP6 RNA 1.fq.gz", "0:150 1:150", "A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633", 150, 150, null, null, 1438540045, 1272310670, 1290121053, 1436739799, 59633, "SRX23527798", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30604, "SRR27865243", "SRX23527797", "SRS20377517", "SRP488009", "PRJNA1073183", "Transcriptome of SEMA5A  MT ATP6  ZNF662  and KDM4C in zebrafish embryos", "PRJNA1073183", "Other", null, null, null, null, "Embryos transcriptome", "Embryos transcriptome", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con RNA", "1", "1", "con RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP488009", null, null, "con-RNA_1.fq.gz con-RNA_2.fq.gz", "fastq fastq", 6733158900.0, 22443863.0, "con RNA 1.fq.gz", "0:150 1:150", "A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220", 150, 150, null, null, 1766014369, 1595337569, 1610127771, 1761604971, 74220, "SRX23527797", "SRS20377517", "SRA1797184", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-04", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30716, "SRR28342048", "SRX23948605", "SRS20750294", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag RESA CLIP input B3", "3xflag RESA CLIP input B3 AGN003279", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002510|replicate ref:AGN003279|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 input|replicate label short:RESA CLIP Upf1 #3737 input B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag RESA HITS CLIP input B3", "AGR004059", "AGR004059", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004059_R1.fastq AGR004059_R2.fastq", "fastq fastq", 15446715026.0, 51148063.0, "AGR004059 R1.fastq.zst", "0:151 1:151", "A:4298384942;C:3080575022;G:4004069877;T:4063619821;N:65364", 151, 151, null, null, 4298384942, 3080575022, 4004069877, 4063619821, 65364, "SRX23948605", "SRS20750294", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30717, "SRR28342039", "SRX23948614", "SRS20750302", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 R843C RESA HITS CLIP B1", "3xflag upf1 R843C RESA HITS CLIP B1 AGN003273", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003273|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 R843C RESA HITS CLIP B1", "AGR004053", "AGR004053", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004053_R1.fastq AGR004053_R2.fastq", "fastq fastq", 10545264992.0, 34918096.0, "AGR004053 R1.fastq.zst", "0:151 1:151", "A:2943441620;C:2155828506;G:2709854276;T:2736095568;N:45022", 151, 151, null, null, 2943441620, 2155828506, 2709854276, 2736095568, 45022, "SRX23948614", "SRS20750302", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30718, "SRR28342040", "SRX23948613", "SRS20750303", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 C126S RESA HITS CLIP B2", "3xflag upf1 C126S RESA HITS CLIP B2 AGN003282", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003282|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 C126S RESA HITS CLIP B2", "AGR004062", "AGR004062", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004062_R1.fastq AGR004062_R2.fastq", "fastq fastq", 11134300590.0, 36868545.0, "AGR004062 R1.fastq.zst", "0:151 1:151", "A:3063023630;C:2386509106;G:2925940275;T:2758782993;N:44586", 151, 151, null, null, 3063023630, 2386509106, 2925940275, 2758782993, 44586, "SRX23948613", "SRS20750303", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30719, "SRR28342041", "SRX23948612", "SRS20750301", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 C126S RESA HITS CLIP B1", "3xflag upf1 C126S RESA HITS CLIP B1 AGN003281", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003281|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 C126S RESA HITS CLIP B1", "AGR004061", "AGR004061", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004061_R1.fastq AGR004061_R2.fastq", "fastq fastq", 13368435586.0, 44266343.0, "AGR004061 R1.fastq.zst", "0:151 1:151", "A:3603822055;C:2659540495;G:3591989409;T:3513026539;N:57088", 151, 151, null, null, 3603822055, 2659540495, 3591989409, 3513026539, 57088, "SRX23948612", "SRS20750301", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30720, "SRR28342042", "SRX23948611", "SRS20750300", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 G495R/G497E RESA HITS CLIP B2", "3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGN003278", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003278|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 G495R/G497E RESA HITS CLIP B2", "AGR004058", "AGR004058", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004058_R1.fastq AGR004058_R2.fastq", "fastq fastq", 13750586084.0, 45531742.0, "AGR004058 R1.fastq.zst", "0:151 1:151", "A:3775460380;C:2748834924;G:3672092546;T:3554141983;N:56251", 151, 151, null, null, 3775460380, 2748834924, 3672092546, 3554141983, 56251, "SRX23948611", "SRS20750300", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30721, "SRR28342043", "SRX23948610", "SRS20750299", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 G495R/G497E RESA HITS CLIP B1", "3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGN003277", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003277|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 G495R/G497E RESA HITS CLIP B1", "AGR004057", "AGR004057", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004057_R1.fastq AGR004057_R2.fastq", "fastq fastq", 10708529212.0, 35458706.0, "AGR004057 R1.fastq.zst", "0:151 1:151", "A:2983511099;C:2231542625;G:2842811089;T:2650619142;N:45257", 151, 151, null, null, 2983511099, 2231542625, 2842811089, 2650619142, 45257, "SRX23948610", "SRS20750299", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30722, "SRR28342044", "SRX23948609", "SRS20750297", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag gfp RESA HITS CLIP B1", "3xflag gfp RESA HITS CLIP B1 AGN002579", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001970|replicate ref:AGN002579|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:gfp CLIP|replicate label short:gfp CLIP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag gfp RESA HITS CLIP B1", "AGR003308", "AGR003308", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003308_R1.fastq AGR003308_R2.fastq", "fastq fastq", 507167460.0, 2510730.0, "AGR003308 R1.fastq.zst", "0:101 1:101", "A:156207937;C:97169427;G:111291367;T:142479104;N:19625", 101, 101, null, null, 156207937, 97169427, 111291367, 142479104, 19625, "SRX23948609", "SRS20750297", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30723, "SRR28342045", "SRX23948608", "SRS20750298", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag RESA HITS CLIP input B4", "3xflag RESA CLIP input B4 AGN003267", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002504|replicate ref:AGN003267|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 input|replicate label short:RESA CLIP Upf1 #3650 input B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag RESA HITS CLIP input B4", "AGR004047", "AGR004047", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004047_R2.fastq AGR004047_R1.fastq", "fastq fastq", 19396379142.0, 64226421.0, "AGR004047 R1.fastq.zst", "0:151 1:151", "A:5606633601;C:3872715770;G:4910603410;T:5006345083;N:81278", 151, 151, null, null, 5606633601, 3872715770, 4910603410, 5006345083, 81278, "SRX23948608", "SRS20750298", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30724, "SRR28342046", "SRX23948607", "SRS20750295", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf3b RESA HITS CLIP B2", "3xflag upf3b RESA HITS CLIP B2 AGN002796", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002796|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf3b RESA HITS CLIP B2", "AGR003554", "AGR003554", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003554_R1.fastq AGR003554_R2.fastq", "fastq fastq", 9047261244.0, 44788422.0, "AGR003554 R1.fastq.zst", "0:101 1:101", "A:2711585737;C:1825740983;G:2076537283;T:2433050799;N:346442", 101, 101, null, null, 2711585737, 1825740983, 2076537283, 2433050799, 346442, "SRX23948607", "SRS20750295", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30725, "SRR28342047", "SRX23948606", "SRS20750296", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf3b RESA HITS CLIP B1", "3xflag upf3b RESA HITS CLIP B1 AGN002795", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002795|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf3b RESA HITS CLIP B1", "AGR003549", "AGR003549", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003549_R1.fastq AGR003549_R2.fastq", "fastq fastq", 9617196770.0, 47609885.0, "AGR003549 R1.fastq.zst", "0:101 1:101", "A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990", 101, 101, null, null, 2856263963, 1963091501, 2218118010, 2579364306, 358990, "SRX23948606", "SRS20750296", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30726, "SRR28342049", "SRX23948604", "SRS20750292", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf3a RESA HITS CLIP B2", "3xflag upf3a RESA HITS CLIP B2 AGN002792", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002792|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf3a RESA HITS CLIP B2", "AGR003566", "AGR003566", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003566_R1.fastq AGR003566_R2.fastq", "fastq fastq", 50318544410.0, 249101705.0, "AGR003566 R1.fastq.zst", "0:101 1:101", "A:14930547705;C:10295739682;G:11624332741;T:13466693890;N:1230392", 101, 101, null, null, 14930547705, 10295739682, 11624332741, 13466693890, 1230392, "SRX23948604", "SRS20750292", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30727, "SRR28342050", "SRX23948603", "SRS20750293", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf3a RESA HITS CLIP B1", "3xflag upf3a RESA HITS CLIP B1 AGN002791", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002791|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf3a RESA HITS CLIP B1", "AGR003545", "AGR003545", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003545_R1.fastq AGR003545_R2.fastq", "fastq fastq", 10770959564.0, 53321582.0, "AGR003545 R1.fastq.zst", "0:101 1:101", "A:3207646854;C:2186852059;G:2481889724;T:2894165865;N:405062", 101, 101, null, null, 3207646854, 2186852059, 2481889724, 2894165865, 405062, "SRX23948603", "SRS20750293", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30728, "SRR28342051", "SRX23948602", "SRS20750291", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf2 RESA HITS CLIP B2", "3xflag upf2 RESA HITS CLIP B2 AGN002788", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002788|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf2 RESA HITS CLIP B2", "AGR003541", "AGR003541", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003541_R1.fastq AGR003541_R2.fastq", "fastq fastq", 9471117440.0, 46886720.0, "AGR003541 R1.fastq.zst", "0:101 1:101", "A:2852420143;C:1898246719;G:2136843599;T:2583254674;N:352305", 101, 101, null, null, 2852420143, 1898246719, 2136843599, 2583254674, 352305, "SRX23948602", "SRS20750291", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30729, "SRR28342052", "SRX23948601", "SRS20750290", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf2 RESA HITS CLIP B1", "3xflag upf2 RESA HITS CLIP B1 AGN002787", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002787|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf2 RESA HITS CLIP B1", "AGR003542", "AGR003542", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003542_R1.fastq AGR003542_R2.fastq", "fastq fastq", 10845546044.0, 53690822.0, "AGR003542 R1.fastq.zst", "0:101 1:101", "A:3277705832;C:2154122837;G:2449408891;T:2963913264;N:395220", 101, 101, null, null, 3277705832, 2154122837, 2449408891, 2963913264, 395220, "SRX23948601", "SRS20750290", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30730, "SRR28342053", "SRX23948600", "SRS20750289", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 RESA HITS CLIP B5", "3xflag upf1 RESA HITS CLIP B5 AGN003270", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003270|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 RESA HITS CLIP B5", "AGR004050", "AGR004050", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004050_R1.fastq AGR004050_R2.fastq", "fastq fastq", 11823214534.0, 39149717.0, "AGR004050 R1.fastq.zst", "0:151 1:151", "A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480", 151, 151, null, null, 3184473505, 2558650081, 3236214151, 2843828317, 48480, "SRX23948600", "SRS20750289", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30731, "SRR28342054", "SRX23948599", "SRS20750288", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 RESA HITS CLIP B4", "3xflag upf1 RESA HITS CLIP B4 AGN003269", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003269|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 RESA HITS CLIP B4", "AGR004049", "AGR004049", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004049_R1.fastq AGR004049_R2.fastq", "fastq fastq", 14371221754.0, 47586827.0, "AGR004049 R1.fastq.zst", "0:151 1:151", "A:3983698498;C:2912453835;G:3805806498;T:3669203887;N:59036", 151, 151, null, null, 3983698498, 2912453835, 3805806498, 3669203887, 59036, "SRX23948599", "SRS20750288", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30732, "SRR28342055", "SRX23948598", "SRS20750287", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 RESA HITS CLIP B3", "3xflag upf1 RESA HITS CLIP B3 AGN002798", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002798|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 RESA HITS CLIP B3", "AGR003555", "AGR003555", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003555_R1.fastq AGR003555_R2.fastq", "fastq fastq", 13605076932.0, 67351866.0, "AGR003555 R1.fastq.zst", "0:101 1:101", "A:3996372048;C:2823464384;G:3156030119;T:3628752419;N:457962", 101, 101, null, null, 3996372048, 2823464384, 3156030119, 3628752419, 457962, "SRX23948598", "SRS20750287", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30733, "SRR28342056", "SRX23948597", "SRS20750283", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 RESA HITS CLIP B2", "3xflag upf1 RESA HITS CLIP B2 AGN002784", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002784|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 RESA HITS CLIP B2", "AGR003552", "AGR003552", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003552_R1.fastq AGR003552_R2.fastq", "fastq fastq", 10762870878.0, 53281539.0, "AGR003552 R1.fastq.zst", "0:101 1:101", "A:3170047840;C:2223795927;G:2504911576;T:2863700088;N:415447", 101, 101, null, null, 3170047840, 2223795927, 2504911576, 2863700088, 415447, "SRX23948597", "SRS20750283", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30734, "SRR28342057", "SRX23948596", "SRS20750286", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 RESA HITS CLIP B1", "3xflag upf1 RESA HITS CLIP B1 AGN002577", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001968|replicate ref:AGN002577|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:upf1 CLIP|replicate label short:upf1 CLIP B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 RESA HITS CLIP B1", "AGR003306", "AGR003306", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR003306_R1.fastq AGR003306_R2.fastq", "fastq fastq", 529433718.0, 2620959.0, "AGR003306 R1.fastq.zst", "0:101 1:101", "A:157881697;C:106579975;G:122214915;T:142736640;N:20491", 101, 101, null, null, 157881697, 106579975, 122214915, 142736640, 20491, "SRX23948596", "SRS20750286", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30735, "SRR28342058", "SRX23948595", "SRS20750284", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag upf1 R843C RESA HITS CLIP B2", "3xflag upf1 R843C RESA HITS CLIP B2 AGN003274", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003274|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag upf1 R843C RESA HITS CLIP B2", "AGR004054", "AGR004054", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004054_R1.fastq AGR004054_R2.fastq", "fastq fastq", 12067359790.0, 39958145.0, "AGR004054 R1.fastq.zst", "0:151 1:151", "A:3301899297;C:2532414363;G:3161463027;T:3071532640;N:50463", 151, 151, null, null, 3301899297, 2532414363, 3161463027, 3071532640, 50463, "SRX23948595", "SRS20750284", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30736, "SRR28342059", "SRX23948594", "SRS20750282", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag RESA CLIP input B2", "3xflag RESA CLIP input B2 AGN003275", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002508|replicate ref:AGN003275|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 input|replicate label short:RESA CLIP Upf1 #3736 input B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag RESA HITS CLIP input B2", "AGR004055", "AGR004055", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004055_R1.fastq AGR004055_R2.fastq", "fastq fastq", 13295917534.0, 44026217.0, "AGR004055 R1.fastq.zst", "0:151 1:151", "A:3866188367;C:2751508227;G:3344357660;T:3333805406;N:57874", 151, 151, null, null, 3866188367, 2751508227, 3344357660, 3333805406, 57874, "SRX23948594", "SRS20750282", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [30737, "SRR28342060", "SRX23948593", "SRS20750285", "SRP495203", "PRJNA1087701", "UPF1 regulates mRNA stability by sensing poorly translated coding sequences   HITS CLIP.", "PRJNA1087701", "Other", "Post transcriptional mRNA regulation shapes gene expression  yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation  uORF content  codon optimality  AU rich elements  microRNA binding sites  and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate  including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated  such as mRNAs with long ORFs  ORF like three primeUTRs  and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.", null, null, null, "3xflag RESA CLIP input B1", "3xflag RESA CLIP input B1 AGN003271", null, "strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002506|replicate ref:AGN003271|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735  3736  3737  3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 input|replicate label short:RESA CLIP Upf1 #3735 input B1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "3xflag RESA HITS CLIP input B1", "AGR004051", "AGR004051", "PCR from library specific RT", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495203", null, null, "AGR004051_R1.fastq AGR004051_R2.fastq", "fastq fastq", 14891006336.0, 49307968.0, "AGR004051 R1.fastq.zst", "0:151 1:151", "A:4241333172;C:3027167277;G:3764089225;T:3858355544;N:61118", 151, 151, null, null, 4241333172, 3027167277, 3764089225, 3858355544, 61118, "SRX23948593", "SRS20750285", "SRA1824033", "Yale University|Genetics", "Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-03-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33326, "SRR29962931", "SRX25444536", "SRS22101407", "SRP521963", "PRJNA1139824", "Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq", "PRJNA1139824", "Other", "Toxicity of sine wave on early zebrafish embryo development", null, null, null, "Embryos m6A transcriptome", "Embryos m6A transcriptome of SW", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zx150 RNAseq", "4", "4", "zx150 RNAseq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP521963", null, null, "zx150_input_1.fq.gz zx150_input_2.fq.gz", "fastq fastq", 11540682300.0, 38468941.0, "zx150 input 1.fq.gz", "0:150 1:150", "A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003", 150, 150, null, null, 3038586049, 2720235923, 2771004747, 3010645578, 210003, "SRX25444536", "SRS22101407", "SRA1931991", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33327, "SRR29962932", "SRX25444535", "SRS22101407", "SRP521963", "PRJNA1139824", "Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq", "PRJNA1139824", "Other", "Toxicity of sine wave on early zebrafish embryo development", null, null, null, "Embryos m6A transcriptome", "Embryos m6A transcriptome of SW", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con RNAseq", "3", "3", "con RNAseq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP521963", null, null, "con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz", "fastq fastq", 11610174300.0, 38700581.0, "con zx150 input 1.fq.gz", "0:150 1:150", "A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827", 150, 150, null, null, 3049654977, 2746004045, 2795023766, 3019280685, 210827, "SRX25444535", "SRS22101407", "SRA1931991", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33328, "SRR29962933", "SRX25444534", "SRS22101407", "SRP521963", "PRJNA1139824", "Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq", "PRJNA1139824", "Other", "Toxicity of sine wave on early zebrafish embryo development", null, null, null, "Embryos m6A transcriptome", "Embryos m6A transcriptome of SW", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zx150 m6A", "2", "2", "zx150 m6A", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP521963", null, null, "zx150_IP_1.fq.gz zx150_IP_2.fq.gz", "fastq fastq", 17410816801.0, 80469610.0, "zx150 IP 1.fq.gz", "0:108.79 1:107.58", "A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583", 108, 107, null, null, 4434870667, 3759430468, 4812205613, 4404166470, 143583, "SRX25444534", "SRS22101407", "SRA1931991", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33329, "SRR29962934", "SRX25444533", "SRS22101407", "SRP521963", "PRJNA1139824", "Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq", "PRJNA1139824", "Other", "Toxicity of sine wave on early zebrafish embryo development", null, null, null, "Embryos m6A transcriptome", "Embryos m6A transcriptome of SW", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con m6A", "1", "1", "con m6A", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP521963", null, null, "con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz", "fastq fastq", 16822889423.0, 77865752.0, "con zx150 IP 1.fq.gz", "0:108.68 1:107.37", "A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001", 108, 107, null, null, 4324048234, 3668630618, 4601614069, 4228151501, 445001, "SRX25444533", "SRS22101407", "SRA1931991", "Sichuan University|West China Second University Hospital", "Sichuan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-07-24", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36663, "SRR800049", "SRX257156", "SRS405710", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq 5azaCyD control", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq 5azaCyD control", "sphere RNAseq 5azaCyD control", "9323X2", "1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, "sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz", "Illumina native", 2563410950.0, 51268219.0, "9323X2 120628 SN141 0513 AD12CFACXX 4", "0:50", "A:663337120;C:603101927;G:752336300;T:542924123;N:1711480", 50, null, null, null, 663337120, 603101927, 752336300, 542924123, 1711480, "SRX257156", "SRS405710", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.65713, null, 0.09976, null, 0.81677, null, 0.81063, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36664, "SRR800046", "SRX257155", "SRS405709", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq 5azaCyD treatment", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq 5azaCyD treatment", "sphere RNAseq 5azaCyD treatment", "9323X1", "1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos  which were then incubated in 100uM 5 AzadCyD until sphere stage and collected.  Embryos injected with water served as control. Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, "sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz", "Illumina native", 2595654550.0, 51913091.0, "9323X1 120628 SN141 0513 AD12CFACXX 4", "0:50", "A:676999669;C:618386951;G:759497082;T:539035799;N:1735049", 50, null, null, null, 676999669, 618386951, 759497082, 539035799, 1735049, "SRX257155", "SRS405709", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.76926, null, 0.12287, null, 0.82408, null, 0.72244, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-03", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36665, "SRR800045", "SRX257154", "SRS405708", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "muscle RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:muscle", null, null, null, null, null, null, null, null, "muscle RNAseq totalRNARibominus", "muscle RNAseq totalRNARibominus", "9084X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 1000", "<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>", "SRP020008", null, null, "muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz", "Illumina native", 3506573750.0, 70131475.0, "9084X1 120420 SN141 0500 AD0TG5ACXX 5", "0:50", "A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806", 50, null, null, null, 872717534, 808774955, 1036781008, 777391447, 10908806, "SRX257154", "SRS405708", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.61428, null, 0.09813, null, 0.89305, null, 0.6908, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Undetermined", "Embryo", "Muscle", "Muscular System"], [36666, "SRR800043", "SRX257153", "SRS405345", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq totalRNARibominus", "sphere RNAseq totalRNARibominus", "7986X2", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, "sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz", "Illumina native", 3029181300.0, 60583626.0, "7986X2 110510 SN141 0338 AB06MWABXX 7", "0:50", "A:768949744;C:733340278;G:903149841;T:623482299;N:259138", 50, null, null, null, 768949744, 733340278, 903149841, 623482299, 259138, "SRX257153", "SRS405345", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.83515, null, 0.15524, null, 0.81209, null, 0.81031, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [36667, "SRR800044", "SRX257153", "SRS405345", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "sphere RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:sphere", null, null, null, null, null, null, null, null, "sphere RNAseq totalRNARibominus", "sphere RNAseq totalRNARibominus", "7986X2", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, "sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz", "Illumina native", 3947123500.0, 78942470.0, "7986X2 110606 SN141 0359 BD0D8KABXX 6", "0:50", "A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861", 50, null, null, null, 1000468440, 957437794, 1171831772, 817292633, 92861, "SRX257153", "SRS405345", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.81283, null, 0.14906, null, 0.81335, null, 0.81698, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-07-22", "Blastula", "Embryo", "Undetermined", "Embryo Imprecise"], [36668, "SRR800037", "SRX257149", "SRS405106", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "egg RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg", null, null, null, null, null, null, null, null, "egg RNAseq totalRNARibominus", "egg RNAseq totalRNARibominus", "7784X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, null, null, 3584440000.0, 71688800.0, "7784X1 110323 SN141 0332 A81FDVABXX 8", "0:50", "A:1013532157;C:812179975;G:992916103;T:765761452;N:50313", 50, null, null, null, 1013532157, 812179975, 992916103, 765761452, 50313, "SRX257149", "SRS405106", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.87304, null, 0.12853, null, 0.81988, null, 0.80407, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [36669, "SRR800038", "SRX257149", "SRS405106", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "egg RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|dev stage:egg", null, null, null, null, null, null, null, null, "egg RNAseq totalRNARibominus", "egg RNAseq totalRNARibominus", "7784X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<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>", "SRP020008", null, null, null, null, 2794240450.0, 55884809.0, "7784X1 110119 SN141 0323 B8162JABXX 8", "0:50", "A:792200981;C:632130044;G:772351331;T:596980885;N:577209", 50, null, null, null, 792200981, 632130044, 772351331, 596980885, 577209, "SRX257149", "SRS405106", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.86104, null, 0.12909, null, 0.82266, null, 0.80894, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-01", "Undetermined", "Embryo", "Undetermined", "Embryo Imprecise"], [42451, "SRR5590336", "SRX2847138", "SRS2220119", "SRP115073", "PRJNA387549", "zebrafish Raw sequence reads", "PRJNA387549", "Metagenomics", "The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.", null, null, null, "without xxx and with difenoconazole", "CK D 50 D 500", null, "strain:AB|isolate:embryo|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:pooled male and female|tissue:whole individual|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Sequencing in zebrafish without xxx and with difenoconazole", "zebrafish RNA Sequencing project", "1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>6</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>", "SRP115073", null, null, "CK_1_1.fq.gz CK_1_2.fq.gz CK_2_1.fq.gz CK_3_1.fq.gz CK_3_2.fq.gz D_500_1_1.fq.gz D_500_1_2.fq.gz D_500_2_1.fq.gz D_500_2_2.fq.gz D_500_3_1.fq.gz D_500_3_2.fq.gz D_50_1_1.fq.gz D_50_1_2.fq.gz D_50_3_2.fq.gz D_50_3_1.fq.gz D_50_2_2.fq.gz D_50_2_1.fq.gz CK_2_2.fq.gz", "fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq", 81797448900.0, 272658163.0, "zebrafish RNA Seq", "0:150 1:150", "A:21743331485;C:19042575463;G:19378823851;T:21630253992;N:2464109", 150, 150, null, null, 21743331485, 19042575463, 19378823851, 21630253992, 2464109, "SRX2847138", "SRS2220119", "SRA564978", "China Agricultural University|College of Science", "China Agricultural University", 2, 0.91941, 0.92018, 0.10515, 0.10533, 0.67939, 0.68552, 0.46739, 0.46494, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-04-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [43660, "SRR6003528", "SRX3158823", "SRS2490160", "SRP116760", "PRJNA401346", "Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos", "PRJNA401346", "Other", "To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.", null, null, "100 embyos micorinjected with morphorlinos of miR 462", "Danio rerio embryos", "462MO 48hpf", null, "strain:AB|dev stage:48hpf|sex:not applicable|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:micorinjected with morphorlinos of miR 462|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: 48hpf embryos", "462MO 48hpf", "462MO 48hpf", "Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer\u00a1\u00afs recommendations and indexcodes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP116760", null, null, null, null, 3643659000.0, 14574636.0, "M462MO48 1.fq.gz", "0:125 1:125", "A:929370426;C:890981335;G:907736720;T:914809265;N:761254", 125, 125, null, null, 929370426, 890981335, 907736720, 914809265, 761254, "SRX3158823", "SRS2490160", "SRA605241", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.94745, 0.94585, 0.03062, 0.0299, 0.71005, 0.7167, 0.47212, 0.46832, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "nebnext", "bulk", "unknown", "unknown", null, "China", "2017-09-05", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43661, "SRR6003529", "SRX3158822", "SRS2490159", "SRP116760", "PRJNA401346", "Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos", "PRJNA401346", "Other", "To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.", null, null, "100 embyos of uninjected control", "Danio rerio embryos", "Control 48hpf", null, "strain:AB|dev stage:48hpf|sex:not applicable|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:uninjected control|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: 48hpf embryos", "Control 48hpf", "Control 48hpf", "Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer\u00a1\u00afs recommendations and indexcodes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP116760", null, null, null, null, 3723608000.0, 14894432.0, "Contr48 2.fq.gz", "0:125 1:125", "A:947710287;C:910496767;G:932389849;T:932231152;N:779945", 125, 125, null, null, 947710287, 910496767, 932389849, 932231152, 779945, "SRX3158822", "SRS2490159", "SRA605241", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.94491, 0.94085, 0.0282, 0.02794, 0.70928, 0.71636, 0.46153, 0.4685, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "nebnext", "bulk", "unknown", "unknown", null, "China", "2017-09-05", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43662, "SRR6003530", "SRX3158821", "SRS2490158", "SRP116760", "PRJNA401346", "Raw sequence reads of miR 462/miR 731 knockdwon zebrafish embryos", "PRJNA401346", "Other", "To elucidate the biological roles of miR 462 731 during embryonic development  two morpholinos MOs targeting the mature sequence of miR 462 and miR 731  respectively  were microinjected into zebrafish embryos. A total of 100 embryos of uninjected control  injected with miR 462 MO or injected with miR 731 MO were collected at xxx hpf  respectively  for RNA Seq.", null, null, "100 embyos micorinjected with morphorlinos of miR 731", "Danio rerio embryos", "731MO 48hpf", null, "strain:AB|dev stage:48hpf|sex:not determined|tissue:embryos|biomaterial provider:Key Laboratory of Freshwater Animal Breeding  College of Fishery  Huazhong Agricultural University|collected by:Chun Xiao Huang|sample type:whole embryo|treatment:micorinjected with morphorlinos of miR 731|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: 48hpf embryos", "731MO 48hpf", "731MO 48hpf", "Sequencing libraries were generated using NEBNext? Ultra? RNA LibraryPrep Kit for Illumina? NEB  USA following manufacturer\u00a1\u00afs recommendations and indexcodes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP116760", null, null, null, null, 3700848750.0, 14803395.0, "M731MO48 2.fq.gz", "0:125 1:125", "A:939687783;C:909029785;G:925521644;T:925836207;N:773331", 125, 125, null, null, 939687783, 909029785, 925521644, 925836207, 773331, "SRX3158821", "SRS2490158", "SRA605241", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.94623, 0.94506, 0.02919, 0.02927, 0.71583, 0.72342, 0.47105, 0.47193, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "nebnext", "bulk", "unknown", "unknown", null, "China", "2017-09-05", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [47607, "SRR6996532", "SRX3931184", "SRS3164482", "SRP137031", "PRJNA432757", "zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage", "PRJNA432757", "Other", "To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.", null, null, null, "maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 2", "marcksbMZ shield rep2", null, "strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 2", "MZmarcksb shield PE150 rep2", "MZmarcksb shield PE150 rep2", "The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP137031", null, null, "marcksbMZ2_shield_R1.fastq.bz2 marcksbMZ2_shield_R2.fastq.bz2", "fastq fastq", 957075410.0, 3388133.0, "marcksbMZ2 shield R2.fastq.bz2", "0:141.21 1:141.27", "A:252634407;C:225426820;G:225127111;T:253882486;N:4586", 141, 141, null, null, 252634407, 225426820, 225127111, 253882486, 4586, "SRX3931184", "SRS3164482", "SRA688612", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.9602, 0.96488, 0.04777, 0.04815, 0.76753, 0.7697, 0.48813, 0.4867, 150, 151, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-04-12", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47608, "SRR6996479", "SRX3931150", "SRS3164467", "SRP137031", "PRJNA432757", "zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage", "PRJNA432757", "Other", "To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.", null, null, null, "maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 1", "marcksbMZ shield rep1", null, "strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 1", "MZmarcksb shield PE150 rep1", "MZmarcksb shield PE150 rep1", "The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP137031", null, null, "marcksbMZ1_shield_R2.fastq.bz2 marcksbMZ1_shield_R1.fastq.bz2", "fastq fastq", 1298313857.0, 4880467.0, "marcksbMZ1 shield R2.fastq.bz2", "0:132.94 1:133.09", "A:343658239;C:305189492;G:304679186;T:344779644;N:7296", 132, 133, null, null, 343658239, 305189492, 304679186, 344779644, 7296, "SRX3931150", "SRS3164467", "SRA688589", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.95673, 0.96117, 0.05347, 0.05421, 0.76751, 0.76936, 0.48125, 0.48179, 130, 130, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-04-12", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47609, "SRR6987273", "SRX3926781", "SRS3160495", "SRP137031", "PRJNA432757", "zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage", "PRJNA432757", "Other", "To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.", null, null, null, "WT whole embryos at shield stage from Danio rerio", "WT1 shield", null, "strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: WT embryos at shield stage replicate 2", "wt shield PE rep2", "wt shield PE rep2", "The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina MiSeq", null, "SRP137031", null, null, "WT2_shield_R1.fastq.bz2 WT2_shield_R2.fastq.bz2", "fastq fastq", 1076081986.0, 3852554.0, "WT2 shield R1.fastq.bz2", "0:139.62 1:139.70", "A:280164367;C:257377429;G:257794541;T:280730273;N:15376", 139, 139, null, null, 280164367, 257377429, 257794541, 280730273, 15376, "SRX3926781", "SRS3160495", "SRA687978", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.93567, 0.94244, 0.04042, 0.04049, 0.77455, 0.77697, 0.48487, 0.47998, 151, 151, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-04-12", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [47610, "SRR6933827", "SRX3878878", "SRS3118690", "SRP137031", "PRJNA432757", "zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage", "PRJNA432757", "Other", "To better understand the compensation network in MZmarcksb  we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.", null, null, null, null, "WT1 shield rep1", null, "strain:AB|dev stage:shield stage|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: WT embryos at shield stage replicate 1", "wt shield PE rep1", "wt shield PE rep1", "The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen  China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1  g. The average final library size is 309 bp.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP137031", null, null, "WT1_shield_R1.fastq.bz2 WT1_shield_R2.fastq.bz2", "fastq fastq", 892273276.0, 3407597.0, "WT1 shield R1.fastq.bz2", "0:130.75 1:131.10", "A:235694986;C:210056075;G:210344332;T:236174033;N:3850", 130, 131, null, null, 235694986, 210056075, 210344332, 236174033, 3850, "SRX3878878", "SRS3118690", "SRA681078", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.95143, 0.95581, 0.04389, 0.04405, 0.77143, 0.77319, 0.48336, 0.48263, 118, 118, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-04-03", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [49248, "SRR7881079", "SRX4719723", "SRS3804945", "SRP162200", "PRJNA492186", "Danio rerio Genome sequencing", "PRJNA492186", "Other", "The transcriptome of zebrafish mutant and wt embryos.", null, null, null, "wt", "wt", null, "strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:normal body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq data of wt", "RNA Seq data of wt", "RNA Seq data of wt", "For each sample  mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162200", null, null, "WT-blu_L5_I392.R1.clean.fastq.gz WT-blu_L5_I392.R2.clean.fastq.gz", "fastq fastq", 3703694250.0, 14814777.0, "WT blu L5 I392.R2.clean.fastq.gz", "0:125 1:125", "A:966446794;C:893928928;G:885838907;T:957360869;N:118752", 125, 125, null, null, 966446794, 893928928, 885838907, 957360869, 118752, "SRX4719723", "SRS3804945", "SRA779493", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.97308, 0.97256, 0.07482, 0.07588, 0.70431, 0.70595, 0.49836, 0.5007, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-20", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [49249, "SRR7881080", "SRX4719722", "SRS3804946", "SRP162200", "PRJNA492186", "Danio rerio Genome sequencing", "PRJNA492186", "Other", "The transcriptome of zebrafish mutant and wt embryos.", null, null, null, "mutant", "zmynd10 mutant", null, "strain:TU|age:30h|sex:not determined|tissue:whole body|phenotype:curve body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq data of zmynd10 mutant", "RNA Seq data of zmynd10 mutant", "RNA Seq data of zmynd10 mutant", "For each sample  mRNA was extracted from the whole body of one individual and the standard RNA Seq library was constructed and subjected to Illumina PE125 sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162200", null, null, "MT-blu_L5_I393.R1.clean.fastq.gz MT-blu_L5_I393.R2.clean.fastq.gz", "fastq fastq", 4156063750.0, 16624255.0, "MT blu L5 I393.R2.clean.fastq.gz", "0:125 1:125", "A:1084666899;C:1001943643;G:994799272;T:1074520227;N:133709", 125, 125, null, null, 1084666899, 1001943643, 994799272, 1074520227, 133709, "SRX4719722", "SRS3804946", "SRA779493", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.97259, 0.97221, 0.07667, 0.0775, 0.70084, 0.70199, 0.4768, 0.48903, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-20", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [51069, "SRR8926593", "SRX5707650", "SRS4646935", "SRP192957", "PRJNA515990", "zebrafish miR 430 KO transcriptome", "PRJNA515990", "Other", "MiR 430 is considered an important regulator during embryonic development  but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement  germ layer specification  axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets  we collected the WT  miR 430 /  and rescued embryos at shield stage and performed transcriptome sequencing.", null, null, "miR 430 /  embryos were injected with miR 430 rescued  20 embryos at shield stage were collected for RNA seq analsysis", "Rescued", "R6", null, "strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:Rescued by miR 430 injection|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish miR 430 KO", "5065335", "5065335", "high throughtput sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP192957", null, null, "R6_GTGGCC_L001_R1_001.fastq.gz R6_GTGGCC_L001_R2_001.fastq.gz R6_GTGGCC_L002_R1_001.fastq.gz R6_GTGGCC_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 3784504800.0, 18922524.0, "R6 GTGGCC L001 R1 001.fastq.gz", "0:100 1:100", "A:998174818;C:911994688;G:866970560;T:1007223918;N:140816", 100, 100, null, null, 998174818, 911994688, 866970560, 1007223918, 140816, "SRX5707650", "SRS4646935", "SRA876443", "Sun Yat-Sen University|School of Life Sciences", "Sun Yat-Sen University", 2, 0.95548, 0.95511, 0.07794, 0.079, 0.75603, 0.75933, 0.48812, 0.48112, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-04-18", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [51070, "SRR8926594", "SRX5707649", "SRS4646934", "SRP192957", "PRJNA515990", "zebrafish miR 430 KO transcriptome", "PRJNA515990", "Other", "MiR 430 is considered an important regulator during embryonic development  but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement  germ layer specification  axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets  we collected the WT  miR 430 /  and rescued embryos at shield stage and performed transcriptome sequencing.", null, null, "20 miR 430 /  embryos at shield stage were collected for RNA seq analsysis", "MiR 430 / ", "M6", null, "strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:miR 430 was deleted by TALENs|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish miR 430 KO", "5065334", "5065334", "high throughtput sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP192957", null, null, "M6_GTGAAA_L002_R2_001.fastq.gz M6_GTGAAA_L002_R1_001.fastq.gz M6_GTGAAA_L001_R2_001.fastq.gz M6_GTGAAA_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 3957356200.0, 19786781.0, "M6 GTGAAA L001 R1 001.fastq.gz", "0:100 1:100", "A:1047013756;C:951740713;G:905354408;T:1053098995;N:148328", 100, 100, null, null, 1047013756, 951740713, 905354408, 1053098995, 148328, "SRX5707649", "SRS4646934", "SRA876443", "Sun Yat-Sen University|School of Life Sciences", "Sun Yat-Sen University", 2, 0.9588, 0.95721, 0.07699, 0.07822, 0.75422, 0.75903, 0.47996, 0.48477, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-04-18", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 132, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"experiment.library_selection\" = :p1 order by rowid limit 101", "params": {"p0": "Embryo", "p1": "RT-PCR"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 81, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 49, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&experiment.library_strategy=OTHER", "selected": false}, {"value": "RIP-Seq", "label": "RIP-Seq", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&experiment.library_strategy=RIP-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 132, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "RT-PCR", "label": 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"hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 132, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "Embryo", "label": "Embryo", "count": 132, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=RT-PCR", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": 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"tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 124, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Embryo&experiment.library_selection=RT-PCR&tissue_curation_coarse=Embryo+Imprecise", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 2, "toggle_url": 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