{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_strategy = \"OTHER\" and technology = \"unknown\"", "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:8|replicate:replicate A|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "HMW fraction 4hpf replica A", "Library 8", "Library 8", "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_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz", "fastq fastq", 12066108000.0, 39954000.0, "BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz", "0:151 1:151", "A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936", 151, 151, null, null, 3060316371, 3136678983, 2965588104, 2902920606, 603936, "SRX23160981", "SRS20111138", "SRA1775336", "University of Basel|Biozentrum Basel", "University of Basel", 2, 0.01336, 5e-05, 0.00027, 0.0, 0.99143, 0.99983, 0.40418, 0.125, 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"], [29213, "SRR27489729", "SRX23160980", "SRS20111142", "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: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. 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, "RNA product", "control RNA library", "RNA mMessage MPRA library", null, "strain:not applicable|age:not applicable|dev stage:not applicable|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:not applicable|biomaterial provider:Schier lab|collected by:Madalena M. 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. 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 C", "MPRA repC 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: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"], [29746, "SRR27467679", "SRX23139227", "SRS20090270", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary BS R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  BS  rep2", "EV02003", "EV02003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02003.R1.fastq.gz EV02003.R2.fastq.gz", "fastq fastq", 1031891720.0, 3416860.0, "EV02003.R1.fastq.gz", "0:151 1:151", "A:264464363;C:153440613;G:408557241;T:205367487;N:62016", 151, 151, null, null, 264464363, 153440613, 408557241, 205367487, 62016, "SRX23139227", "SRS20090270", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 0.0, 0.00019, 0.0, 0.00015, 1.0, 0.99993, null, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29755, "SRR27467688", "SRX23139218", "SRS20090261", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary DM R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  DM  rep2", "EV02002", "EV02002", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02002.R1.fastq.gz EV02002.R2.fastq.gz", "fastq fastq", 861320308.0, 2852054.0, "EV02002.R1.fastq.gz", "0:151 1:151", "A:205625519;C:162178974;G:334206312;T:159256900;N:52603", 151, 151, null, null, 205625519, 162178974, 334206312, 159256900, 52603, "SRX23139218", "SRS20090261", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00049, 0.0, 0.00027, 1.0, 0.99947, null, 0.44444, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29756, "SRR27467689", "SRX23139217", "SRS20090260", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary mock R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  mock  rep2", "EV02001", "EV02001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02001.R1.fastq.gz EV02001.R2.fastq.gz", "fastq fastq", 520371066.0, 1723083.0, "EV02001.R1.fastq.gz", "0:151 1:151", "A:116107273;C:90896560;G:218652568;T:94682244;N:32421", 151, 151, null, null, 116107273, 90896560, 218652568, 94682244, 32421, "SRX23139217", "SRS20090260", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00086, 0.0, 0.00078, 0.99995, 0.99981, 0.0, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [31943, "SRR28790250", "SRX24354554", "SRS21112322", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  high dose  dsRNA2", "GSM8228804", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  high dose  dsRNA2", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA", "GSM8228804", "GSM8228804: Zebrafish  Riboseq  high dose  dsRNA2; Danio rerio; OTHER", "GSM8228804 r1", "GSM8228804", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "dsR_2.R1.raw.fastq.gz dsR_2.R2.raw.fastq.gz", "fastq fastq", 15877367026.0, 52574063.0, "GSM8228804 r1", "0:151 1:151", "A:3017944891;C:2902425937;G:7224440180;T:2731881397;N:674621", 151, 151, null, null, 3017944891, 2902425937, 7224440180, 2731881397, 674621, "SRX24354554", "SRS21112322", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31944, "SRR28790251", "SRX24354553", "SRS21112321", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  high dose  dsRNA1", "GSM8228803", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  high dose  dsRNA1", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA", "GSM8228803", "GSM8228803: Zebrafish  Riboseq  high dose  dsRNA1; Danio rerio; OTHER", "GSM8228803 r1", "GSM8228803", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "dsR_1.R1.raw.fastq.gz dsR_1.R2.raw.fastq.gz", "fastq fastq", 13027928774.0, 43138837.0, "GSM8228803 r1", "0:151 1:151", "A:2538099201;C:2400262316;G:5852047273;T:2236961902;N:558082", 151, 151, null, null, 2538099201, 2400262316, 5852047273, 2236961902, 558082, "SRX24354553", "SRS21112321", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31945, "SRR28790252", "SRX24354552", "SRS21112320", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  high dose  uninj2", "GSM8228802", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  high dose  uninj2", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected", "GSM8228802", "GSM8228802: Zebrafish  Riboseq  high dose  uninj2; Danio rerio; OTHER", "GSM8228802 r1", "GSM8228802", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "un_2.R1.raw.fastq.gz un_2.R2.raw.fastq.gz", "fastq fastq", 13637060056.0, 45155828.0, "GSM8228802 r1", "0:151 1:151", "A:2596015831;C:2388366938;G:6201010197;T:2451085273;N:581817", 151, 151, null, null, 2596015831, 2388366938, 6201010197, 2451085273, 581817, "SRX24354552", "SRS21112320", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31946, "SRR28790253", "SRX24354551", "SRS21112319", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  high dose  uninj1", "GSM8228801", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  high dose  uninj1", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected", "GSM8228801", "GSM8228801: Zebrafish  Riboseq  high dose  uninj1; Danio rerio; OTHER", "GSM8228801 r1", "GSM8228801", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "un_1.R1.raw.fastq.gz un_1.R2.raw.fastq.gz", "fastq fastq", 13499333560.0, 44699780.0, "GSM8228801 r1", "0:151 1:151", "A:2587725963;C:2439789499;G:6080777505;T:2390460459;N:580134", 151, 151, null, null, 2587725963, 2439789499, 6080777505, 2390460459, 580134, "SRX24354551", "SRS21112319", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31947, "SRR28790254", "SRX24354550", "SRS21112318", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  low dose  dsRNA2", "GSM8228800", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  low dose  dsRNA2", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA", "GSM8228800", "GSM8228800: Zebrafish  Riboseq  low dose  dsRNA2; Danio rerio; OTHER", "GSM8228800 r1", "GSM8228800", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "dsR_2.raw.1.fastq.gz dsR_2.raw.2.fastq.gz", "fastq fastq", 13335544766.0, 44157433.0, "GSM8228800 r1", "0:151 1:151", "A:2383528724;C:2262795235;G:6593680813;T:2094730217;N:809777", 151, 151, null, null, 2383528724, 2262795235, 6593680813, 2094730217, 809777, "SRX24354550", "SRS21112318", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31948, "SRR28790255", "SRX24354549", "SRS21112317", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  low dose  dsRNA1", "GSM8228799", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  low dose  dsRNA1", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:dsRNA", "GSM8228799", "GSM8228799: Zebrafish  Riboseq  low dose  dsRNA1; Danio rerio; OTHER", "GSM8228799 r1", "GSM8228799", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "dsR_1.raw.1.fastq.gz dsR_1.raw.2.fastq.gz", "fastq fastq", 12530433302.0, 41491501.0, "GSM8228799 r1", "0:151 1:151", "A:2300207705;C:2164355626;G:6050556625;T:2014558360;N:754986", 151, 151, null, null, 2300207705, 2164355626, 6050556625, 2014558360, 754986, "SRX24354549", "SRS21112317", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31949, "SRR28790256", "SRX24354548", "SRS21112316", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  low dose  uninj2", "GSM8228798", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  low dose  uninj2", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected", "GSM8228798", "GSM8228798: Zebrafish  Riboseq  low dose  uninj2; Danio rerio; OTHER", "GSM8228798 r1", "GSM8228798", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "un_2.raw.1.fastq.gz un_2.raw.2.fastq.gz", "fastq fastq", 12132018896.0, 40172248.0, "GSM8228798 r1", "0:151 1:151", "A:2225485331;C:2027579165;G:5953072417;T:1925141784;N:740199", 151, 151, null, null, 2225485331, 2027579165, 5953072417, 1925141784, 740199, "SRX24354548", "SRS21112316", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [31950, "SRR28790257", "SRX24354547", "SRS21112315", "SRP503769", "PRJNA1104180", "Double stranded RNA triggers a distinct integrated stress response in the early embryo [RNA seq  Ribo seq]", "GSE265771", "Other", "Double stranded RNA dsRNA is associated with virus infections and is present as by products during the transcription of synthetic mRNA  which has been widely used in gene gain of function studies and serves as a core component in emerging mRNA based therapies1 4. The presence of dsRNA in host cells induces an integrated stress response that functions to prevent virus replication and infection5 6. Unlike differentiated cells  undifferentiated cells adopt a distinct defense strategy against RNA virus infection7  but the mechanism is unclear. We show a previously unidentified response triggered by dsRNA in the early embryo. Although dsRNA causes a global protein translation inhibition in a PKR eIF2a independent manner and leads to developmental delay and cell necrosis  it also strongly induces p53 activation  which then upregulates Interferon Stimulated Genes independently of interferon ligands. Importantly  we demonstrate that the burst of p53 signaling dose not result in cell death but functions as a protective mechanism against deleterious translation blockage by slowing down global protein degradation via ISGylation. Our work has identified a distinct dsRNA induced stress response in the embryo  reflecting an ancient innate immune memory before the establishment of the IFN system. It also raises the provocative question as to the original protective role of p53 during evolution. Overall design: To characterize the distribution of ribosomes on mRNA  we performed Ribosome profiling Ribo seq analysis with RNA seq on dsRNA injected embryos.", null, null, null, "Zebrafish  Riboseq  low dose  uninj1", "GSM8228797", null, "source name:whole embryo|tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected|geo loc name:missing|collection date:missing", "Zebrafish  Riboseq  low dose  uninj1", "The library underwent quality control assessment  and was subjected to Illumina Novaseq 6000 sequencing. Bio informatics analysis of RIBOseq profilling was performed to analyze the library data. Assembly: GRCz10 Supplementary files format and content: Excel file includes raw counts for each Sample Library strategy: Ribo seq", "whole embryo", null, "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and 3\u2019 blocked linker 5\u2019 rApp CTGTAGGCACCATCAAT NH2 3\u2019 was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "tissue:whole embryo|developmental stage:50% epiboly stage|cell type:embryonic cell|genotype:wild type|treatment:uninjected", "GSM8228797", "GSM8228797: Zebrafish  Riboseq  low dose  uninj1; Danio rerio; OTHER", "GSM8228797 r1", "GSM8228797", "1", "Both control group and dsRNA injected embryos at xxx hpf were thoroughly lysed on ice using lysis buffer.The lysate was then centrifuged at 12000g at 4\u00b0C for 10 minutes to remove cellular components  including undigested material such as cell nuclei.Then  RNaseI was added to the supernatant and incubated at 25\u00b0C for 30 minutes to digest RNA  while the RNA fragments protected by ribosomes were preserved. Subsequently  an RNA inhibitor was added to terminate the digestion reaction. The lysate was subjected to sucrose density gradient centrifugation  and fractions containing single peaks at 260nm wavelength around the 80S monosome region were collected. The collected mixture was then thoroughly lysed using Trizol for RNA extraction. RNA fragments within the size range of 26 34nt was separated using polyacrylamide gel electrophoresis without xxx  and the corresponding bands were collected. The recovered bands were subjected to ligation reaction  where a preadenylylated and three prime blocked linker five prime rApp CTGTAGGCACCATCAAT NH2 three prime was attached to the three prime end of the RNA. The ligated products were then recovered by performing polyacrylamide gel electrophoresis. Subsequently  the recovered RNA fragments were reverse transcribed using a reverse primer to obtain extended cDNA molecules. The purified cDNA was subjected to circularization by using CircLigase Epicentre  CL4111K  resulting in the formation of circular cDNA molecules. To remove residual rRNA components in the cDNA  a method involving hybridization with complementary primers specific to rRNA and subsequent heat denaturation was employed. The remaining circularized cDNA was then amplified through PCR  and barcode sequences were incorporated.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP503769", null, null, "un_1.raw.1.fastq.gz un_1.raw.2.fastq.gz", "fastq fastq", 10423454802.0, 34514751.0, "GSM8228797 r1", "0:151 1:151", "A:1931094519;C:1788894999;G:5028533789;T:1674294221;N:637274", 151, 151, null, null, 1931094519, 1788894999, 5028533789, 1674294221, 637274, "SRX24354547", "SRS21112315", "SRA1852128", "ShanDong University", "ShanDong University", null, null, null, null, null, null, null, null, null, null, null, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-04-24", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [32508, "SRR29290248", "SRX24807391", "SRS21522263", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  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applicable|age:3 month|dev stage:3 month|collection date:2023 08 23|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Exposed to tire wear particles above 120 mesh excretion for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L3 1", "L3 1", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TLSA-1L.R1.fq.gz TLSA-1L.R2.fq.gz", "fastq fastq", 6188928300.0, 20629761.0, "TLSA 1L.R1.fq.gz", "0:150 1:150", "A:1584479312;C:1464260894;G:1549296685;T:1590644766;N:246643", 150, 150, null, null, 1584479312, 1464260894, 1549296685, 1590644766, 246643, "SRX24807388", "SRS21522260", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32512, "SRR29290252", "SRX24807387", "SRS21522259", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "15 days experimental group parallel 3", "liver transcriptome", "L2 3", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 08|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposed to 120 or above tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L2 3", "L2 3", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TLFC1-3L.R1.fq.gz TLFC1-3L.R2.fq.gz", "fastq fastq", 6367070400.0, 21223568.0, "TLFC1 3L.R1.fq.gz", "0:150 1:150", "A:1579430230;C:1587605262;G:1613210542;T:1586578782;N:245584", 150, 150, null, null, 1579430230, 1587605262, 1613210542, 1586578782, 245584, "SRX24807387", "SRS21522259", "SRA1889615", "Qingdao University of Science and technology|College of marine science and 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particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L2 2", "L2 2", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TLFB1-3L.R1.fq.gz TLFB1-3L.R2.fq.gz", "fastq fastq", 6996653100.0, 23322177.0, "TLFB1 3L.R1.fq.gz", "0:150 1:150", "A:1803878205;C:1678057588;G:1715367000;T:1799170285;N:180022", 150, 150, null, null, 1803878205, 1678057588, 1715367000, 1799170285, 180022, "SRX24807386", "SRS21522258", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32514, "SRR29290254", "SRX24807385", "SRS21522257", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "15 days experimental group parallel 1", "liver transcriptome", "L2 1", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 08|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 14|experiment description:Exposed to 120 or above tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L2 1", "L2 1", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TLFA6-7L.R1.fq.gz TLFA6-7L.R2.fq.gz", "fastq fastq", 6109509300.0, 20365031.0, "TLFA6 7L.R1.fq.gz", "0:150 1:150", "A:1525902154;C:1507317327;G:1549698641;T:1526193716;N:397462", 150, 150, null, null, 1525902154, 1507317327, 1549698641, 1526193716, 397462, "SRX24807385", "SRS21522257", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", 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"strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 10|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L6 3", "L6 3", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TSFC1-3L.R1.fq.gz TSFC1-3L.R2.fq.gz", "fastq fastq", 6857466600.0, 22858222.0, "TSFC1 3L.R1.fq.gz", "0:150 1:150", "A:1755136176;C:1642995302;G:1688825155;T:1770233592;N:276375", 150, 150, null, null, 1755136176, 1642995302, 1688825155, 1770233592, 276375, "SRX24807380", "SRS21522252", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32520, "SRR29290260", "SRX24807379", "SRS21522251", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "15 days experimental group parallel 2", "liver transcriptome", "L6 2", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 10|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 15|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L6 2", "L6 2", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TSFB1-3L.R1.fq.gz TSFB1-3L.R2.fq.gz", "fastq fastq", 7250329800.0, 24167766.0, "TSFB1 3L.R1.fq.gz", "0:150 1:150", "A:1825803037;C:1766132142;G:1813762639;T:1844348502;N:283480", 150, 150, null, null, 1825803037, 1766132142, 1813762639, 1844348502, 283480, "SRX24807379", "SRS21522251", "SRA1889615", "Qingdao 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14|experiment description:Exposure to 40 60 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L6 1", "L6 1", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TSFA1-3L.R1.fq.gz TSFA1-3L.R2.fq.gz", "fastq fastq", 6257752800.0, 20859176.0, "TSFA1 3L.R1.fq.gz", "0:150 1:150", "A:1588621972;C:1490176001;G:1573465475;T:1605244426;N:244926", 150, 150, null, null, 1588621972, 1490176001, 1573465475, 1605244426, 244926, "SRX24807378", "SRS21522250", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32522, "SRR29290262", "SRX24807377", "SRS21522249", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "30 days experimental group parallel 3", "liver transcriptome", "L5 3", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 13|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L5 3", "L5 3", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TMSC-5L.R1.fq.gz TMSC-5L.R2.fq.gz", "fastq fastq", 6227549100.0, 20758497.0, "TMSC 5L.R1.fq.gz", "0:150 1:150", "A:1601663321;C:1467885504;G:1549957271;T:1607796578;N:246426", 150, 150, null, null, 1601663321, 1467885504, 1549957271, 1607796578, 246426, "SRX24807377", "SRS21522249", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32523, "SRR29290263", "SRX24807376", "SRS21522248", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "30 days experimental group parallel 2", "liver transcriptome", "L5 2", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L5 2", "L5 2", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TMSB-3L.R1.fq.gz TMSB-3L.R2.fq.gz", "fastq fastq", 5889087600.0, 19630292.0, "TMSB 3L.R1.fq.gz", "0:150 1:150", "A:1507527640;C:1395223794;G:1475557797;T:1510549619;N:228750", 150, 150, null, null, 1507527640, 1395223794, 1475557797, 1510549619, 228750, "SRX24807376", "SRS21522248", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32524, "SRR29290264", "SRX24807375", "SRS21522247", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "30 days experimental group parallel 1", "liver transcriptome", "L5 1", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 24|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Exposed to tire wear particles 80 100 mesh excretion for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L5 1", "L5 1", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TMSA-1L.R1.fq.gz TMSA-1L.R2.fq.gz", "fastq fastq", 6438780300.0, 21462601.0, "TMSA 1L.R1.fq.gz", "0:150 1:150", "A:1651115385;C:1542448300;G:1589631411;T:1655336061;N:249143", 150, 150, null, null, 1651115385, 1542448300, 1589631411, 1655336061, 249143, "SRX24807375", "SRS21522247", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32525, "SRR29290265", "SRX24807374", "SRS21522246", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "15 days experimental group parallel 3", "liver transcriptome", "L4 3", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 09|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 16|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L4 3", "L4 3", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TMFC1-3L.R1.fq.gz TMFC1-3L.R2.fq.gz", "fastq fastq", 6083883300.0, 20279611.0, "TMFC1 3L.R1.fq.gz", "0:150 1:150", "A:1510698562;C:1511134044;G:1540128451;T:1521679717;N:242526", 150, 150, null, null, 1510698562, 1511134044, 1540128451, 1521679717, 242526, "SRX24807374", "SRS21522246", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32526, "SRR29290266", "SRX24807373", "SRS21522245", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "15 days experimental group parallel 2", "liver transcriptome", "L4 2", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 09|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 15|experiment description:Exposure to 80 100 mesh tire wear particles for 15 days|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L4 2", "L4 2", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "TMFB1-3L.R1.fq.gz TMFB1-3L.R2.fq.gz", "fastq fastq", 5908013700.0, 19693379.0, "TMFB1 3L.R1.fq.gz", "0:150 1:150", "A:1507137134;C:1415511620;G:1463261753;T:1521838130;N:265063", 150, 150, null, null, 1507137134, 1415511620, 1463261753, 1521838130, 265063, "SRX24807373", "SRS21522245", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32527, "SRR29290267", "SRX24807372", "SRS21522244", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "Control parallel 2", "liver transcriptome", "L1 2", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 11|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 12|experiment description:Sample from control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L1 2", "L1 2", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "FCFB1-3L.R1.fq.gz FCFB1-3L.R2.fq.gz", "fastq fastq", 6637856700.0, 22126189.0, "FCFB1 3L.R1.fq.gz", "0:150 1:150", "A:1714779556;C:1575842801;G:1628771136;T:1718209685;N:253522", 150, 150, null, null, 1714779556, 1575842801, 1628771136, 1718209685, 253522, "SRX24807372", "SRS21522244", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32528, "SRR29290268", "SRX24807371", "SRS21522243", "SRP511901", "PRJNA1120203", "Study of liver transcriptome in zebrafish  May 29 '24", "PRJNA1120203", "Other", "Liver of the transcriptome data from zebrafish exposed to small car tire wear particles", null, null, "Control parallel 1", "liver transcriptome", "L1 1", null, "strain:not applicable|isolate:not applicable|breed:zebrafish|cultivar:not applicable|ecotype:not applicable|age:3 month|dev stage:3 month|collection date:2023 08 11|geo loc name:China|sex:not collected|tissue:liver|birth date:2023 05 11|experiment description:Sample from control group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish liver", "L1 1", "L1 1", "Total RNA was extracted from the zebrafish liver tissue using a commercial RNA extraction kit following the manufacturer's instructions.The prepared library was sequenced on an Illumina HiSeq platform  generating paired end reads.", null, null, "OTHER", "METATRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP511901", null, null, "FCFA1-3L.R1.fq.gz FCFA1-3L.R2.fq.gz", "fastq fastq", 7360809900.0, 24536033.0, "FCFA1 3L.R1.fq.gz", "0:150 1:150", "A:1885247052;C:1777296186;G:1818891778;T:1879185198;N:189686", 150, 150, null, null, 1885247052, 1777296186, 1818891778, 1879185198, 189686, "SRX24807371", "SRS21522243", "SRA1889615", "Qingdao University of Science and technology|College of marine science and biological engineeri", "Qingdao University of Science and technology", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-05", "Adult", "Adult", "Liver", "Liver and Biliary System"], [33990, "SRR31030860", "SRX26416598", "SRS22936450", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep4 minus", "GSM8578751", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578751", "GSM8578751: ZF NES GAPDH Rep4 minus; Danio rerio; OTHER", "GSM8578751 r1", "GSM8578751", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep4_minus.R1.fq.gz ZF_NES_GAPDH_Rep4_minus.R2.fq.gz", "fastq fastq", 1100578200.0, 3668594.0, "GSM8578751 r1", "0:150 1:150", "A:287878221;C:249390946;G:265835736;T:297454600;N:18697", 150, 150, null, null, 287878221, 249390946, 265835736, 297454600, 18697, "SRX26416598", "SRS22936450", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33991, "SRR31030861", "SRX26416597", "SRS22936451", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 plus", "GSM8578750", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578750", "GSM8578750: ZF NES GAPDH Rep3 plus; Danio rerio; OTHER", "GSM8578750 r1", "GSM8578750", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep3_plus.R1.fq.gz ZF_NES_GAPDH_Rep3_plus.R2.fq.gz", "fastq fastq", 1231779300.0, 4105931.0, "GSM8578750 r1", "0:150 1:150", "A:322256597;C:278991471;G:297394980;T:333116282;N:19970", 150, 150, null, null, 322256597, 278991471, 297394980, 333116282, 19970, "SRX26416597", "SRS22936451", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33992, "SRR31030862", "SRX26416596", "SRS22936449", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep3 minus", "GSM8578749", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578749", "GSM8578749: ZF NES GAPDH Rep3 minus; Danio rerio; OTHER", "GSM8578749 r1", "GSM8578749", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep3_minus.R1.fq.gz ZF_NES_GAPDH_Rep3_minus.R2.fq.gz", "fastq fastq", 1002124500.0, 3340415.0, "GSM8578749 r1", "0:150 1:150", "A:262024969;C:227163761;G:242157218;T:270761424;N:17128", 150, 150, null, null, 262024969, 227163761, 242157218, 270761424, 17128, "SRX26416596", "SRS22936449", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33993, "SRR31030863", "SRX26416595", "SRS22936448", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 plus", "GSM8578748", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578748", "GSM8578748: ZF NES GAPDH Rep2 plus; Danio rerio; OTHER", "GSM8578748 r1", "GSM8578748", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep2_plus.R1.fq.gz ZF_NES_GAPDH_Rep2_plus.R2.fq.gz", "fastq fastq", 1051565100.0, 3505217.0, "GSM8578748 r1", "0:150 1:150", "A:275784945;C:237523425;G:253300749;T:284937948;N:18033", 150, 150, null, null, 275784945, 237523425, 253300749, 284937948, 18033, "SRX26416595", "SRS22936448", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33994, "SRR31030864", "SRX26416594", "SRS22936447", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep2 minus", "GSM8578747", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578747", "GSM8578747: ZF NES GAPDH Rep2 minus; Danio rerio; OTHER", "GSM8578747 r1", "GSM8578747", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep2_minus.R1.fq.gz ZF_NES_GAPDH_Rep2_minus.R2.fq.gz", "fastq fastq", 1021837200.0, 3406124.0, "GSM8578747 r1", "0:150 1:150", "A:268290250;C:230525208;G:245949056;T:277056045;N:16641", 150, 150, null, null, 268290250, 230525208, 245949056, 277056045, 16641, "SRX26416594", "SRS22936447", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33995, "SRR31030865", "SRX26416593", "SRS22936446", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 plus", "GSM8578746", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:plus DBF", "GSM8578746", "GSM8578746: ZF NES GAPDH Rep1 plus; Danio rerio; OTHER", "GSM8578746 r1", "GSM8578746", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep1_plus.R1.fq.gz ZF_NES_GAPDH_Rep1_plus.R2.fq.gz", "fastq fastq", 1093620300.0, 3645401.0, "GSM8578746 r1", "0:150 1:150", "A:285989719;C:247805250;G:264181043;T:295625946;N:18342", 150, 150, null, null, 285989719, 247805250, 264181043, 295625946, 18342, "SRX26416593", "SRS22936446", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33996, "SRR31030866", "SRX26416592", "SRS22936445", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF NES GAPDH Rep1 minus", "GSM8578745", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF NES GAPDH Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo NES|treatment:minus DBF", "GSM8578745", "GSM8578745: ZF NES GAPDH Rep1 minus; Danio rerio; OTHER", "GSM8578745 r1", "GSM8578745", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_NES_GAPDH_Rep1_minus.R1.fq.gz ZF_NES_GAPDH_Rep1_minus.R2.fq.gz", "fastq fastq", 911747100.0, 3039157.0, "GSM8578745 r1", "0:150 1:150", "A:239833349;C:205185786;G:218897710;T:247814511;N:15744", 150, 150, null, null, 239833349, 205185786, 218897710, 247814511, 15744, "SRX26416592", "SRS22936445", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33997, "SRR31030867", "SRX26416591", "SRS22936444", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 plus", "GSM8578744", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep4 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578744", "GSM8578744: ZF H2B MALAT1 Rep4 plus; Danio rerio; OTHER", "GSM8578744 r1", "GSM8578744", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep4_plus.R1.fq.gz ZF_H2B_MALAT1_Rep4_plus.R2.fq.gz", "fastq fastq", 842103300.0, 2807011.0, "GSM8578744 r1", "0:150 1:150", "A:204870477;C:222752099;G:215404135;T:199062275;N:14314", 150, 150, null, null, 204870477, 222752099, 215404135, 199062275, 14314, "SRX26416591", "SRS22936444", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33998, "SRR31030868", "SRX26416590", "SRS22936442", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep4 minus", "GSM8578743", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578743", "GSM8578743: ZF H2B MALAT1 Rep4 minus; Danio rerio; OTHER", "GSM8578743 r1", "GSM8578743", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep4_minus.R1.fq.gz ZF_H2B_MALAT1_Rep4_minus.R2.fq.gz", "fastq fastq", 1166375100.0, 3887917.0, "GSM8578743 r1", "0:150 1:150", "A:283781955;C:308660466;G:298298204;T:275614377;N:20098", 150, 150, null, null, 283781955, 308660466, 298298204, 275614377, 20098, "SRX26416590", "SRS22936442", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [33999, "SRR31030869", "SRX26416589", "SRS22936443", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 plus", "GSM8578742", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep3 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578742", "GSM8578742: ZF H2B MALAT1 Rep3 plus; Danio rerio; OTHER", "GSM8578742 r1", "GSM8578742", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep3_plus.R1.fq.gz ZF_H2B_MALAT1_Rep3_plus.R2.fq.gz", "fastq fastq", 1159439400.0, 3864798.0, "GSM8578742 r1", "0:150 1:150", "A:282055391;C:306842216;G:296569227;T:273952570;N:19996", 150, 150, null, null, 282055391, 306842216, 296569227, 273952570, 19996, "SRX26416589", "SRS22936443", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34000, "SRR31030870", "SRX26416588", "SRS22936440", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep3 minus", "GSM8578741", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep3 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578741", "GSM8578741: ZF H2B MALAT1 Rep3 minus; Danio rerio; OTHER", "GSM8578741 r1", "GSM8578741", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep3_minus.R1.fq.gz ZF_H2B_MALAT1_Rep3_minus.R2.fq.gz", "fastq fastq", 1008297600.0, 3360992.0, "GSM8578741 r1", "0:150 1:150", "A:245277585;C:266840408;G:257911846;T:238251305;N:16456", 150, 150, null, null, 245277585, 266840408, 257911846, 238251305, 16456, "SRX26416588", "SRS22936440", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34001, "SRR31030871", "SRX26416587", "SRS22936441", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 plus", "GSM8578740", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep2 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578740", "GSM8578740: ZF H2B MALAT1 Rep2 plus; Danio rerio; OTHER", "GSM8578740 r1", "GSM8578740", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep2_plus.R1.fq.gz ZF_H2B_MALAT1_Rep2_plus.R2.fq.gz", "fastq fastq", 1419263400.0, 4730878.0, "GSM8578740 r1", "0:150 1:150", "A:345302268;C:375591885;G:362956395;T:335387828;N:25024", 150, 150, null, null, 345302268, 375591885, 362956395, 335387828, 25024, "SRX26416587", "SRS22936441", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34002, "SRR31030872", "SRX26416586", "SRS22936439", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep2 minus", "GSM8578739", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep2 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF", "GSM8578739", "GSM8578739: ZF H2B MALAT1 Rep2 minus; Danio rerio; OTHER", "GSM8578739 r1", "GSM8578739", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep2_minus.R1.fq.gz ZF_H2B_MALAT1_Rep2_minus.R2.fq.gz", "fastq fastq", 1249910700.0, 4166369.0, "GSM8578739 r1", "0:150 1:150", "A:304074828;C:330741431;G:319677748;T:295395235;N:21458", 150, 150, null, null, 304074828, 330741431, 319677748, 295395235, 21458, "SRX26416586", "SRS22936439", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34003, "SRR31030873", "SRX26416585", "SRS22936438", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 plus", "GSM8578738", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep1 plus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.", "tissue:2 dpf embryos|genotype:Halo H2B|treatment:plus DBF", "GSM8578738", "GSM8578738: ZF H2B MALAT1 Rep1 plus; Danio rerio; OTHER", "GSM8578738 r1", "GSM8578738", "1", "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", null, "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539182", null, null, "ZF_H2B_MALAT1_Rep1_plus.R1.fq.gz ZF_H2B_MALAT1_Rep1_plus.R2.fq.gz", "fastq fastq", 1257872700.0, 4192909.0, "GSM8578738 r1", "0:150 1:150", "A:306022947;C:332851039;G:321699513;T:297277788;N:21413", 150, 150, null, null, 306022947, 332851039, 321699513, 297277788, 21413, "SRX26416585", "SRS22936438", "SRA1993027", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", "Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [34004, "SRR31030874", "SRX26416584", "SRS22936437", "SRP539182", "PRJNA1174121", "Quantification of subcellular RNA localization through direct detection of RNA oxidation", "GSE279714", "Other", "Across cell types and organisms  thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B MALAT1 Rep1 minus", "GSM8578737", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B MALAT1 Rep1 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. The extent of oxidation was then calculated at the gene level using PIGPEN software.", null, "pubmed:39605352;pubmed:40037712", null, "ZF H2B GAPDH Rep4 minus", "GSM8578735", null, "source name:2 dpf embryos|tissue:2 dpf embryos|genotype:Halo H2B|treatment:minus DBF|geo loc name:missing|collection date:missing", "ZF H2B GAPDH Rep4 minus", "OINC seq Oxidation Induced Nucleotide Conversion sequencing Adapters were trimmed from reads using Cutadapt. RNA oxidation events as seen as mutations were quantified using PIGPEN https://github.com/TaliaferroLab/OINC seq Assembly: hg38 and GRCz11 Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.", "2 dpf embryos", null, "RNA was extracted using Trizol and DNase treated for 30 min at 37C. Single amplicon libraries were constructed using gene specific RT PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.", "HeLa cells were cultured in DMEM + pen/strep + 10% FBS. 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The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes  multiple proximity based techniques have been developed in which RNAs near a localized bait protein are specifically labeled  facilitating their biotinylation and purification. However  these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations  we developed Oxidation Induced Nucleotide Conversion sequencing OINC seq. In OINC seq  RNAs near a genetically encoded  localized bait protein are specifically oxidized in a photo controllable manner. These oxidation events are then directly detected and quantified using high throughput sequencing and our software package  PIGPEN  without xxx need for biotin mediated enrichment. We demonstrate that OINC seq can induce and quantify RNA oxidation with high specificity in a dose  and light dependent manner. We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. 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We further show the spatial specificity of OINC seq by using it to quantify subcellular transcriptomes associated with the cytoplasm  ER  and the inner and outer membranes of mitochondria. Finally  using transgenic zebrafish  we demonstrate that OINC seq allows proximity mediated RNA labeling in live animals. In sum  OINC seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems. Overall design: Cells and tissues were treated with and without xxx that drive localized RNA oxidation at a variety of subcellular locations  including treatment with the singlet oxygen producer Halo DBF and treatment with green light to activate Halo DBF. 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