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52 rows where devstage_curation = "Blastula" and experiment.library_selection = "RT-PCR"

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tissue_curation 3

experiment.library_strategy 3

tissue_curation_coarse 2

experiment.library_layout 2

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 52 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Blastula · 52 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29212 29212 SRR27489728 SRX23160981 SRS20111138 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.     polysome fraction HMW fraction 4hpf replica A MPRA repA fractions 8 9 4hpf   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:8|replicate:replicate A|BioSampleModel:Model organism or animal                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29213 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. 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.     polysome fraction LMW fraction 4hpf replica A MPRA repA fractions 6 7 4hpf   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:7|replicate:replicate A|BioSampleModel:Model organism or animal                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29214 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.     polysome fraction 80S fraction 4hpf replica A MPRA repA fractions 4 5 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29224 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.     input sample Total 4hpf replica A MPRA repA input 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29225 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.     polysome fraction HMW fraction 4hpf replica C MPRA repC fractions 8 9 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29226 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.     polysome fraction LMW fraction 4hpf replica C MPRA repC fractions 6 7 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29227 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.     polysome fraction 80S fraction 4hpf replica C MPRA repC fractions 4 5 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29228 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.     input sample Total 4hpf replica C MPRA repC input 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29242 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.     polysome fraction HMW fraction 4hpf replica B MPRA repB fractions 8 9 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29243 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.     polysome fraction LMW fraction 4hpf replica B MPRA repB fractions 6 7 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29244 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.     polysome fraction 80S fraction 4hpf replica B MPRA repB fractions 4 5 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29245 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.     input sample Total 4hpf replica B MPRA repB input 4hpf   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                 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.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     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     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   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
30599 30599 SRR27865238 SRX23527802 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con MO 6 6 con MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-KDM_1.fq.gz con-KDM_2.fq.gz fastq fastq 7088132100.0 23627107.0 con KDM 1.fq.gz 0:150 1:150 A:1893419600;C:1649526065;G:1662549202;T:1882459200;N:178033 150 150     1893419600 1649526065 1662549202 1882459200 178033 SRX23527802 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30600 30600 SRR27865239 SRX23527801 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 KDM4C MO 5 5 KDM4C MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     KDM-MO_1.fq.gz KDM-MO_2.fq.gz fastq fastq 7876840500.0 26256135.0 KDM MO 1.fq.gz 0:150 1:150 A:2104173142;C:1831662159;G:1843980192;T:2096831538;N:193469 150 150     2104173142 1831662159 1843980192 2096831538 193469 SRX23527801 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30601 30601 SRR27865240 SRX23527800 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 ZNF662 MO 4 4 ZNF662 MO     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     znf547-MO_1.fq.gz znf547-MO_2.fq.gz fastq fastq 7573815300.0 25246051.0 znf547 MO 1.fq.gz 0:150 1:150 A:2014197761;C:1766587259;G:1782217029;T:2010540623;N:272628 150 150     2014197761 1766587259 1782217029 2010540623 272628 SRX23527800 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30602 30602 SRR27865241 SRX23527799 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 SEMA5A RNA 3 3 SEMA5A RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     semRNA_1.fq.gz semRNA_2.fq.gz fastq fastq 5575566000.0 18585220.0 semRNA 1.fq.gz 0:150 1:150 A:1456001758;C:1325628099;G:1339796989;T:1454076989;N:62165 150 150     1456001758 1325628099 1339796989 1454076989 62165 SRX23527799 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30603 30603 SRR27865242 SRX23527798 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 MT ATP6 RNA 2 2 MT ATP6 RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     ATP6-RNA_1.fq.gz ATP6-RNA_2.fq.gz fastq fastq 5437771200.0 18125904.0 ATP6 RNA 1.fq.gz 0:150 1:150 A:1438540045;C:1272310670;G:1290121053;T:1436739799;N:59633 150 150     1438540045 1272310670 1290121053 1436739799 59633 SRX23527798 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30604 30604 SRR27865243 SRX23527797 SRS20377517 SRP488009 PRJNA1073183 Transcriptome of SEMA5A MT ATP6 ZNF662 and KDM4C in zebrafish embryos PRJNA1073183 Other         Embryos transcriptome Embryos transcriptome   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNA 1 1 con RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP488009     con-RNA_1.fq.gz con-RNA_2.fq.gz fastq fastq 6733158900.0 22443863.0 con RNA 1.fq.gz 0:150 1:150 A:1766014369;C:1595337569;G:1610127771;T:1761604971;N:74220 150 150     1766014369 1595337569 1610127771 1761604971 74220 SRX23527797 SRS20377517 SRA1797184 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-02-04 Blastula Embryo Embryo Imprecise All anatomical structures
30716 30716 SRR28342048 SRX23948605 SRS20750294 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B3 3xflag RESA CLIP input B3 AGN003279   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002510|replicate ref:AGN003279|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 input|replicate label short:RESA CLIP Upf1 #3737 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B3 AGR004059 AGR004059 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004059_R1.fastq AGR004059_R2.fastq fastq fastq 15446715026.0 51148063.0 AGR004059 R1.fastq.zst 0:151 1:151 A:4298384942;C:3080575022;G:4004069877;T:4063619821;N:65364 151 151     4298384942 3080575022 4004069877 4063619821 65364 SRX23948605 SRS20750294 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30717 30717 SRR28342039 SRX23948614 SRS20750302 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 R843C RESA HITS CLIP B1 3xflag upf1 R843C RESA HITS CLIP B1 AGN003273   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003273|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 R843C RESA HITS CLIP B1 AGR004053 AGR004053 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004053_R1.fastq AGR004053_R2.fastq fastq fastq 10545264992.0 34918096.0 AGR004053 R1.fastq.zst 0:151 1:151 A:2943441620;C:2155828506;G:2709854276;T:2736095568;N:45022 151 151     2943441620 2155828506 2709854276 2736095568 45022 SRX23948614 SRS20750302 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30718 30718 SRR28342040 SRX23948613 SRS20750303 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 C126S RESA HITS CLIP B2 3xflag upf1 C126S RESA HITS CLIP B2 AGN003282   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003282|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 C126S RESA HITS CLIP B2 AGR004062 AGR004062 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004062_R1.fastq AGR004062_R2.fastq fastq fastq 11134300590.0 36868545.0 AGR004062 R1.fastq.zst 0:151 1:151 A:3063023630;C:2386509106;G:2925940275;T:2758782993;N:44586 151 151     3063023630 2386509106 2925940275 2758782993 44586 SRX23948613 SRS20750303 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30719 30719 SRR28342041 SRX23948612 SRS20750301 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 C126S RESA HITS CLIP B1 3xflag upf1 C126S RESA HITS CLIP B1 AGN003281   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002511|replicate ref:AGN003281|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3737 IP|replicate label short:RESA CLIP Upf1 #3737 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 C126S RESA HITS CLIP B1 AGR004061 AGR004061 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004061_R1.fastq AGR004061_R2.fastq fastq fastq 13368435586.0 44266343.0 AGR004061 R1.fastq.zst 0:151 1:151 A:3603822055;C:2659540495;G:3591989409;T:3513026539;N:57088 151 151     3603822055 2659540495 3591989409 3513026539 57088 SRX23948612 SRS20750301 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30720 30720 SRR28342042 SRX23948611 SRS20750300 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 G495R/G497E RESA HITS CLIP B2 3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGN003278   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003278|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 G495R/G497E RESA HITS CLIP B2 AGR004058 AGR004058 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004058_R1.fastq AGR004058_R2.fastq fastq fastq 13750586084.0 45531742.0 AGR004058 R1.fastq.zst 0:151 1:151 A:3775460380;C:2748834924;G:3672092546;T:3554141983;N:56251 151 151     3775460380 2748834924 3672092546 3554141983 56251 SRX23948611 SRS20750300 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30721 30721 SRR28342043 SRX23948610 SRS20750299 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 G495R/G497E RESA HITS CLIP B1 3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGN003277   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002509|replicate ref:AGN003277|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 IP|replicate label short:RESA CLIP Upf1 #3736 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 G495R/G497E RESA HITS CLIP B1 AGR004057 AGR004057 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004057_R1.fastq AGR004057_R2.fastq fastq fastq 10708529212.0 35458706.0 AGR004057 R1.fastq.zst 0:151 1:151 A:2983511099;C:2231542625;G:2842811089;T:2650619142;N:45257 151 151     2983511099 2231542625 2842811089 2650619142 45257 SRX23948610 SRS20750299 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30722 30722 SRR28342044 SRX23948609 SRS20750297 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag gfp RESA HITS CLIP B1 3xflag gfp RESA HITS CLIP B1 AGN002579   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001970|replicate ref:AGN002579|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:gfp CLIP|replicate label short:gfp CLIP B1|BioSampleModel:Model organism or animal                 3xflag gfp RESA HITS CLIP B1 AGR003308 AGR003308 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003308_R1.fastq AGR003308_R2.fastq fastq fastq 507167460.0 2510730.0 AGR003308 R1.fastq.zst 0:101 1:101 A:156207937;C:97169427;G:111291367;T:142479104;N:19625 101 101     156207937 97169427 111291367 142479104 19625 SRX23948609 SRS20750297 SRA1824033 Yale University|Genetics Yale University                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30723 30723 SRR28342045 SRX23948608 SRS20750298 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA HITS CLIP input B4 3xflag RESA CLIP input B4 AGN003267   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002504|replicate ref:AGN003267|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 input|replicate label short:RESA CLIP Upf1 #3650 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B4 AGR004047 AGR004047 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004047_R2.fastq AGR004047_R1.fastq fastq fastq 19396379142.0 64226421.0 AGR004047 R1.fastq.zst 0:151 1:151 A:5606633601;C:3872715770;G:4910603410;T:5006345083;N:81278 151 151     5606633601 3872715770 4910603410 5006345083 81278 SRX23948608 SRS20750298 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30724 30724 SRR28342046 SRX23948607 SRS20750295 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3b RESA HITS CLIP B2 3xflag upf3b RESA HITS CLIP B2 AGN002796   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002796|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf3b RESA HITS CLIP B2 AGR003554 AGR003554 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003554_R1.fastq AGR003554_R2.fastq fastq fastq 9047261244.0 44788422.0 AGR003554 R1.fastq.zst 0:101 1:101 A:2711585737;C:1825740983;G:2076537283;T:2433050799;N:346442 101 101     2711585737 1825740983 2076537283 2433050799 346442 SRX23948607 SRS20750295 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30725 30725 SRR28342047 SRX23948606 SRS20750296 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3b RESA HITS CLIP B1 3xflag upf3b RESA HITS CLIP B1 AGN002795   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002161|replicate ref:AGN002795|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3b pulldown|replicate label short:Upf3b pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf3b RESA HITS CLIP B1 AGR003549 AGR003549 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003549_R1.fastq AGR003549_R2.fastq fastq fastq 9617196770.0 47609885.0 AGR003549 R1.fastq.zst 0:101 1:101 A:2856263963;C:1963091501;G:2218118010;T:2579364306;N:358990 101 101     2856263963 1963091501 2218118010 2579364306 358990 SRX23948606 SRS20750296 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30726 30726 SRR28342049 SRX23948604 SRS20750292 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3a RESA HITS CLIP B2 3xflag upf3a RESA HITS CLIP B2 AGN002792   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002792|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf3a RESA HITS CLIP B2 AGR003566 AGR003566 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003566_R1.fastq AGR003566_R2.fastq fastq fastq 50318544410.0 249101705.0 AGR003566 R1.fastq.zst 0:101 1:101 A:14930547705;C:10295739682;G:11624332741;T:13466693890;N:1230392 101 101     14930547705 10295739682 11624332741 13466693890 1230392 SRX23948604 SRS20750292 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30727 30727 SRR28342050 SRX23948603 SRS20750293 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf3a RESA HITS CLIP B1 3xflag upf3a RESA HITS CLIP B1 AGN002791   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002159|replicate ref:AGN002791|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf3a pulldown|replicate label short:Upf3a pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf3a RESA HITS CLIP B1 AGR003545 AGR003545 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003545_R1.fastq AGR003545_R2.fastq fastq fastq 10770959564.0 53321582.0 AGR003545 R1.fastq.zst 0:101 1:101 A:3207646854;C:2186852059;G:2481889724;T:2894165865;N:405062 101 101     3207646854 2186852059 2481889724 2894165865 405062 SRX23948603 SRS20750293 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30728 30728 SRR28342051 SRX23948602 SRS20750291 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf2 RESA HITS CLIP B2 3xflag upf2 RESA HITS CLIP B2 AGN002788   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002788|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf2 RESA HITS CLIP B2 AGR003541 AGR003541 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003541_R1.fastq AGR003541_R2.fastq fastq fastq 9471117440.0 46886720.0 AGR003541 R1.fastq.zst 0:101 1:101 A:2852420143;C:1898246719;G:2136843599;T:2583254674;N:352305 101 101     2852420143 1898246719 2136843599 2583254674 352305 SRX23948602 SRS20750291 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30729 30729 SRR28342052 SRX23948601 SRS20750290 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf2 RESA HITS CLIP B1 3xflag upf2 RESA HITS CLIP B1 AGN002787   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002157|replicate ref:AGN002787|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf2 pulldown|replicate label short:Upf2 pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf2 RESA HITS CLIP B1 AGR003542 AGR003542 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003542_R1.fastq AGR003542_R2.fastq fastq fastq 10845546044.0 53690822.0 AGR003542 R1.fastq.zst 0:101 1:101 A:3277705832;C:2154122837;G:2449408891;T:2963913264;N:395220 101 101     3277705832 2154122837 2449408891 2963913264 395220 SRX23948601 SRS20750290 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30730 30730 SRR28342053 SRX23948600 SRS20750289 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B5 3xflag upf1 RESA HITS CLIP B5 AGN003270   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003270|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B5 AGR004050 AGR004050 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004050_R1.fastq AGR004050_R2.fastq fastq fastq 11823214534.0 39149717.0 AGR004050 R1.fastq.zst 0:151 1:151 A:3184473505;C:2558650081;G:3236214151;T:2843828317;N:48480 151 151     3184473505 2558650081 3236214151 2843828317 48480 SRX23948600 SRS20750289 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30731 30731 SRR28342054 SRX23948599 SRS20750288 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B4 3xflag upf1 RESA HITS CLIP B4 AGN003269   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002505|replicate ref:AGN003269|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3650 IP|replicate label short:RESA CLIP Upf1 #3650 IP B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B4 AGR004049 AGR004049 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004049_R1.fastq AGR004049_R2.fastq fastq fastq 14371221754.0 47586827.0 AGR004049 R1.fastq.zst 0:151 1:151 A:3983698498;C:2912453835;G:3805806498;T:3669203887;N:59036 151 151     3983698498 2912453835 3805806498 3669203887 59036 SRX23948599 SRS20750288 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30732 30732 SRR28342055 SRX23948598 SRS20750287 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B3 3xflag upf1 RESA HITS CLIP B3 AGN002798   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002798|replicate order:2|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B2|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B3 AGR003555 AGR003555 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003555_R1.fastq AGR003555_R2.fastq fastq fastq 13605076932.0 67351866.0 AGR003555 R1.fastq.zst 0:101 1:101 A:3996372048;C:2823464384;G:3156030119;T:3628752419;N:457962 101 101     3996372048 2823464384 3156030119 3628752419 457962 SRX23948598 SRS20750287 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30733 30733 SRR28342056 SRX23948597 SRS20750283 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B2 3xflag upf1 RESA HITS CLIP B2 AGN002784   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 08 19|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002154|replicate ref:AGN002784|replicate order:1|project label long:3x flag upf1 2 3a 3b RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:3xflag upf1 RESA HITS CLIP|sample label short:Upf1 pulldown|replicate label short:Upf1 pulldown B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B2 AGR003552 AGR003552 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003552_R1.fastq AGR003552_R2.fastq fastq fastq 10762870878.0 53281539.0 AGR003552 R1.fastq.zst 0:101 1:101 A:3170047840;C:2223795927;G:2504911576;T:2863700088;N:415447 101 101     3170047840 2223795927 2504911576 2863700088 415447 SRX23948597 SRS20750283 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30734 30734 SRR28342057 SRX23948596 SRS20750286 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 RESA HITS CLIP B1 3xflag upf1 RESA HITS CLIP B1 AGN002577   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2021 01 05|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS001968|replicate ref:AGN002577|replicate order:1|project label long:3x flag upf1 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper. Control is 3x flag gfp|project label short:3xflag upf1 RESA HITS CLIP|sample label short:upf1 CLIP|replicate label short:upf1 CLIP B1|BioSampleModel:Model organism or animal                 3xflag upf1 RESA HITS CLIP B1 AGR003306 AGR003306 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR003306_R1.fastq AGR003306_R2.fastq fastq fastq 529433718.0 2620959.0 AGR003306 R1.fastq.zst 0:101 1:101 A:157881697;C:106579975;G:122214915;T:142736640;N:20491 101 101     157881697 106579975 122214915 142736640 20491 SRX23948596 SRS20750286 SRA1824033 Yale University|Genetics Yale University                       B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30735 30735 SRR28342058 SRX23948595 SRS20750284 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag upf1 R843C RESA HITS CLIP B2 3xflag upf1 R843C RESA HITS CLIP B2 AGN003274   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002507|replicate ref:AGN003274|replicate order:2|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 IP|replicate label short:RESA CLIP Upf1 #3735 IP B2|BioSampleModel:Model organism or animal                 3xflag upf1 R843C RESA HITS CLIP B2 AGR004054 AGR004054 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004054_R1.fastq AGR004054_R2.fastq fastq fastq 12067359790.0 39958145.0 AGR004054 R1.fastq.zst 0:151 1:151 A:3301899297;C:2532414363;G:3161463027;T:3071532640;N:50463 151 151     3301899297 2532414363 3161463027 3071532640 50463 SRX23948595 SRS20750284 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30736 30736 SRR28342059 SRX23948594 SRS20750282 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B2 3xflag RESA CLIP input B2 AGN003275   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002508|replicate ref:AGN003275|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3736 input|replicate label short:RESA CLIP Upf1 #3736 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B2 AGR004055 AGR004055 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004055_R1.fastq AGR004055_R2.fastq fastq fastq 13295917534.0 44026217.0 AGR004055 R1.fastq.zst 0:151 1:151 A:3866188367;C:2751508227;G:3344357660;T:3333805406;N:57874 151 151     3866188367 2751508227 3344357660 3333805406 57874 SRX23948594 SRS20750282 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
30737 30737 SRR28342060 SRX23948593 SRS20750285 SRP495203 PRJNA1087701 UPF1 regulates mRNA stability by sensing poorly translated coding sequences HITS CLIP. PRJNA1087701 Other Post transcriptional mRNA regulation shapes gene expression yet how cis elements and mRNA translation interface to regulate mRNA stability is poorly understood. We find that strength of translation initiation uORF content codon optimality AU rich elements microRNA binding sites and ORF length function combinatorially to regulate mRNA stability. Machine learning analysis identifies ORF length as the most important conserved feature regulating mRNA decay. We find that Upf1 binds poorly translated and untranslated ORFs which are associated with higher decay rate including mRNAs with uORFs and those with exposed ORFs post stop codons. Our study emphasizes Upf1's converging role in surveilling mRNAs with exposed ORFs that are poorly translated such as mRNAs with long ORFs ORF like three primeUTRs and mRNAs containing uORFs. We propose that Upf1 regulation of poorly/untranslated ORFs provides a unifying mechanism of surveillance in regulating mRNA stability and homeostasis in an EJC independent NMD pathway that we term ORF Mediated Decay OMD.       3xflag RESA CLIP input B1 3xflag RESA CLIP input B1 AGN003271   strain:TU/AB|age:3.5 hpf|dev stage:1k cell|collection date:2022 10 04|geo loc name:USA|sex:pooled male and female|tissue:embryo|genotype:wt|strain maternal:wt|strain paternal:wt|molecule:mRNA|selection:flag bead PD post crosslinking|sample ref:AGS002506|replicate ref:AGN003271|replicate order:1|project label long:3x flag upf1 mutants plasmids 3735 3736 3737 3650 RESA HITS CLIP using V.Yartseva's library. Followed protocol in paper|project label short:upf1 mutant RESA HITS CLIP|sample label short:RESA CLIP Upf1 #3735 input|replicate label short:RESA CLIP Upf1 #3735 input B1|BioSampleModel:Model organism or animal                 3xflag RESA HITS CLIP input B1 AGR004051 AGR004051 PCR from library specific RT     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP495203     AGR004051_R1.fastq AGR004051_R2.fastq fastq fastq 14891006336.0 49307968.0 AGR004051 R1.fastq.zst 0:151 1:151 A:4241333172;C:3027167277;G:3764089225;T:3858355544;N:61118 151 151     4241333172 3027167277 3764089225 3858355544 61118 SRX23948593 SRS20750285 SRA1824033 Yale University|Genetics Yale University                       B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   United States 2024-03-14 Blastula Embryo Embryo Imprecise All anatomical structures
33326 33326 SRR29962931 SRX25444536 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 RNAseq 4 4 zx150 RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_input_1.fq.gz zx150_input_2.fq.gz fastq fastq 11540682300.0 38468941.0 zx150 input 1.fq.gz 0:150 1:150 A:3038586049;C:2720235923;G:2771004747;T:3010645578;N:210003 150 150     3038586049 2720235923 2771004747 3010645578 210003 SRX25444536 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33327 33327 SRR29962932 SRX25444535 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con RNAseq 3 3 con RNAseq     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_input_1.fq.gz con-zx150_input_2.fq.gz fastq fastq 11610174300.0 38700581.0 con zx150 input 1.fq.gz 0:150 1:150 A:3049654977;C:2746004045;G:2795023766;T:3019280685;N:210827 150 150     3049654977 2746004045 2795023766 3019280685 210827 SRX25444535 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33328 33328 SRR29962933 SRX25444534 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 zx150 m6A 2 2 zx150 m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     zx150_IP_1.fq.gz zx150_IP_2.fq.gz fastq fastq 17410816801.0 80469610.0 zx150 IP 1.fq.gz 0:108.79 1:107.58 A:4434870667;C:3759430468;G:4812205613;T:4404166470;N:143583 108 107     4434870667 3759430468 4812205613 4404166470 143583 SRX25444534 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
33329 33329 SRR29962934 SRX25444533 SRS22101407 SRP521963 PRJNA1139824 Toxicity of sine wave on early zebrafish embryo development by m6A and RNA seq PRJNA1139824 Other Toxicity of sine wave on early zebrafish embryo development       Embryos m6A transcriptome Embryos m6A transcriptome of SW   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|collection date:not applicable|geo loc name:not applicable|BioSampleModel:Model organism or animal                 con m6A 1 1 con m6A     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP521963     con-zx150_IP_1.fq.gz con-zx150_IP_2.fq.gz fastq fastq 16822889423.0 77865752.0 con zx150 IP 1.fq.gz 0:108.68 1:107.37 A:4324048234;C:3668630618;G:4601614069;T:4228151501;N:445001 108 107     4324048234 3668630618 4601614069 4228151501 445001 SRX25444533 SRS22101407 SRA1931991 Sichuan University|West China Second University Hospital Sichuan University                       B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-07-24 Blastula Embryo Embryo Imprecise All anatomical structures
36663 36663 SRR800049 SRX257156 SRS405710 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD control   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD control sphere RNAseq 5azaCyD control 9323X2 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_control_SE_9323X2_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2563410950.0 51268219.0 9323X2 120628 SN141 0513 AD12CFACXX 4 0:50 A:663337120;C:603101927;G:752336300;T:542924123;N:1711480 50       663337120 603101927 752336300 542924123 1711480 SRX257156 SRS405710 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.65713   0.09976   0.81677   0.81063   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Blastula Embryo Embryo Imprecise All anatomical structures
36664 36664 SRR800046 SRX257155 SRS405709 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq 5azaCyD treatment   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq 5azaCyD treatment sphere RNAseq 5azaCyD treatment 9323X1 1nl of 1mM 5 AzadCyD was injected into 1 cell stage embryos which were then incubated in 100uM 5 AzadCyD until sphere stage and collected. Embryos injected with water served as control. Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_5azaCyD_treatment_SE_9323X1_120628_SN141_0513_AD12CFACXX_4.txt.gz Illumina native 2595654550.0 51913091.0 9323X1 120628 SN141 0513 AD12CFACXX 4 0:50 A:676999669;C:618386951;G:759497082;T:539035799;N:1735049 50       676999669 618386951 759497082 539035799 1735049 SRX257155 SRS405709 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.76926   0.12287   0.82408   0.72244   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-04-03 Blastula Embryo Embryo Imprecise All anatomical structures
36666 36666 SRR800043 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110510_SN141_0338_AB06MWABXX_7.txt.gz Illumina native 3029181300.0 60583626.0 7986X2 110510 SN141 0338 AB06MWABXX 7 0:50 A:768949744;C:733340278;G:903149841;T:623482299;N:259138 50       768949744 733340278 903149841 623482299 259138 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.83515   0.15524   0.81209   0.81031   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
36667 36667 SRR800044 SRX257153 SRS405345 SRP020008 PRJNA193544 Danio rerio strain:Tubingen Epigenomics PRJNA193544 Other Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand we determined DNAme profiles of zebrafish gametes multiple embryo stages flanking ZGA and somatic muscle and compared them to gene activity and histone modifications. First sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA preventing their precocious expression. Thus zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.   pubmed:23663776 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper. Generic sample from Danio rerio sphere RNAseq totalRNARibominus   strain:Tubingen|label:PE: paired end SE: single end|development stage:sphere                 sphere RNAseq totalRNARibominus sphere RNAseq totalRNARibominus 7986X2 Total RNA was extracted using Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004 ribosomal RNA was depleted using RiboMinus kit A10837 08 Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP020008     sphere_RNAseq_totalRNARibominus_SE_7986X2_110606_SN141_0359_BD0D8KABXX_6.txt.gz Illumina native 3947123500.0 78942470.0 7986X2 110606 SN141 0359 BD0D8KABXX 6 0:50 A:1000468440;C:957437794;G:1171831772;T:817292633;N:92861 50       1000468440 957437794 1171831772 817292633 92861 SRX257153 SRS405345 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.81283   0.14906   0.81335   0.81698   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2015-07-22 Blastula Embryo Undetermined Embryo Imprecise
75644 75644 SRR24752590 SRX20528694 SRS17837826 SRP439887 PRJNA976915 Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976915 Other Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       Embryos 5hpf Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 RNA Seq of Embryo 5hpf Gentanicin 2 2 Embryo 5hpf Gentanicin     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439887     Qingda_1.fq.gz Qingda_2.fq.gz fastq fastq 6985244400.0 23284148.0 Qingda 1.fq.gz 0:150 1:150 A:1634658220;C:1842974934;G:1881072995;T:1626517291;N:20960 150 150     1634658220 1842974934 1881072995 1626517291 20960 SRX20528694 SRS17837826 SRA1645398 Sichuan University|West China Second University Hospital Sichuan University 2 0.96818 0.97235 0.21368 0.21914 0.79265 0.79273 0.53525 0.50366 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75645 75645 SRR24752591 SRX20528693 SRS17837826 SRP439887 PRJNA976915 Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976915 Other Embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       Embryos 5hpf Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 RNA Seq of WT Embryo 5hpf 1 1 WT Embryo 5hpf     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439887     WT-blank_1.fq.gz WT-blank_2.fq.gz fastq fastq 6062337300.0 20207791.0 WT blank 1.fq.gz 0:150 1:150 A:1526499059;C:1498285888;G:1526586728;T:1510947161;N:18464 150 150     1526499059 1498285888 1526586728 1510947161 18464 SRX20528693 SRS17837826 SRA1645398 Sichuan University|West China Second University Hospital Sichuan University 2 0.96896 0.97182 0.02595 0.02539 0.77861 0.77865 0.48078 0.48377 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75646 75646 SRR24754508 SRX20530612 SRS17839502 SRP439912 PRJNA976946 MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976946 Other MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       m6A Embryos 5hpf m6A Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 MeRIP Seq of Embryo 5hpf Gentanicin 2 2 Embryo 5hpf Gentanicin     RIP-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439912     QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz fastq fastq fastq fastq 16015155900.0 53383853.0 QingdaIP 1.fq.gz 0:150 1:150 A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972 150 150     3341079522 3427050846 6045646273 3201293287 85972 SRX20530612 SRS17839502 SRA1645459 Sichuan University|West China Second University Hospital Sichuan University 2 0.75159 0.73659 0.1359 0.13542 0.8117 0.81172 0.51543 0.51251 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures
75647 75647 SRR24754509 SRX20530611 SRS17839502 SRP439912 PRJNA976946 MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model PRJNA976946 Other MeRIP seq for embryotoxicity evaluation of Gentamicin an aminoglycoside antibiotic added to human embryo culture medium using the zebrafish Danio rerio model       m6A Embryos 5hpf m6A Embryos 5hpf   strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal                 MeRIP Seq of WT Embryo 5hpf 1 1 WT Embryo 5hpf     RIP-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 4000   SRP439912     WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz fastq fastq fastq fastq 15326922600.0 51089742.0 WT blankIP 1.fq.gz 0:150 1:150 A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844 150 150     3289509867 3239692571 5510216977 3287142341 360844 SRX20530611 SRS17839502 SRA1645459 Sichuan University|West China Second University Hospital Sichuan University 2 0.71182 0.69789 0.02169 0.02058 0.80409 0.80395 0.47813 0.48125 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2023-05-27 Blastula Embryo Embryo Imprecise All anatomical structures

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