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49 rows where experiment.library_selection = "RT-PCR" and experiment.library_strategy = "OTHER"

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devstage_curation 4

tissue_curation_coarse 2

tissue_curation 2

technology 1

experiment.platform 1

experiment.library_strategy 1

  • OTHER · 49 ✖

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 49 ✖

experiment.library_layout 1

devstage_curation_coarse 1

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
29210 29210 SRR27489726 SRX23160983 SRS20111140 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica A MPRA repA fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:10|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica A Library 10 Library 10 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_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R2_001_MM_1.fastq.gz fastq fastq 13762167482.0 45570091.0 BSSE QGF 206645 HGWLYDSX3 3 MPRA repA fractions 4 5 6hpf CTCTCGTC TATAACCT S10 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3449173111;C:3620318973;G:3412595233;T:3279391764;N:688401 151 151     3449173111 3620318973 3412595233 3279391764 688401 SRX23160983 SRS20111140 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01348 9e-05 0.00033 1e-05 0.99151 0.99973 0.41104 0.57142 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29211 29211 SRR27489727 SRX23160982 SRS20111139 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 6hpf replica A MPRA repA input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:9|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 6hpf replica A Library 9 Library 9 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_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R1_001_MM_1.fastq.gz fastq fastq 13570263998.0 44934649.0 BSSE QGF 206644 HGWLYDSX3 3 MPRA repA input 6hpf TCTCTACT CGCGGTTC S9 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3444180060;C:3577051220;G:3264051077;T:3284343514;N:638127 151 151     3444180060 3577051220 3264051077 3284343514 638127 SRX23160982 SRS20111139 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01809 5e-05 0.00042 0.0 0.99013 0.99985 0.41794 0.57142 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
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
29215 29215 SRR27489731 SRX23160978 SRS20111136 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     RNA product control RNA library RNA mMessage MPRA library   strain:not applicable|age:not applicable|dev stage:not applicable|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:not applicable|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:not applicable|growth protocol:not applicable|sample type:IVT mRNA|sample number:50|replicate:unique sample|BioSampleModel:Model organism or animal                 control RNA library Library 50 Library 50 PCR product was amplified from DNA plasmid pool with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206685_HGWLYDSX3_3_RNA_mMessage_MPRA_library_test_GGTTATAA_GATATCGA_S50_L003_R2_001_MM_1.fastq.gz fastq fastq 16695252486.0 55282293.0 BSSE QGF 206685 HGWLYDSX3 3 RNA mMessage MPRA library test GGTTATAA GATATCGA S50 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4275447149;C:4413405571;G:3936523108;T:4069049357;N:827301 151 151     4275447149 4413405571 3936523108 4069049357 827301 SRX23160978 SRS20111136 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02176 0.00021 0.00058 2e-05 0.99056 0.99933 0.41475 0.48571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29216 29216 SRR27489733 SRX23160976 SRS20111134 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica C MPRA repC fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:48|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica C Library 48 Library 48 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz fastq fastq 16074911568.0 53228184.0 BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275 151 151     4029048727 4167204709 4036912991 3840941866 803275 SRX23160976 SRS20111134 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00795 0.00021 0.00019 2e-05 0.99263 0.99935 0.45247 0.62857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29217 29217 SRR27489734 SRX23160975 SRS20111132 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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 10hpf replica C MPRA repC fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:47|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica C Library 47 Library 47 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz fastq fastq 16211925948.0 53681874.0 BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500 151 151     4078470905 4239434649 4000426230 3892801664 792500 SRX23160975 SRS20111132 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01232 0.00028 0.00027 5e-05 0.99166 0.99926 0.4522 0.61904 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29218 29218 SRR27489735 SRX23160974 SRS20111131 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. 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 10hpf replica C MPRA repC fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:46|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica C Library 46 Library 46 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz fastq fastq 18761117310.0 62122905.0 BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979 151 151     4746221682 4940258209 4549993563 4523714877 928979 SRX23160974 SRS20111131 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01785 0.0002 0.00043 3e-05 0.9908 0.99951 0.45866 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29219 29219 SRR27489736 SRX23160973 SRS20111130 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica C MPRA repC input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:45|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 10hpf replica C Library 45 Library 45 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz fastq fastq 15148053334.0 50159117.0 BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975 151 151     3877492548 4007711111 3560735163 3701356537 757975 SRX23160973 SRS20111130 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02196 3e-05 0.00062 1e-05 0.98944 0.99993 0.4404 0.66666 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29220 29220 SRR27489737 SRX23160972 SRS20111129 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica C MPRA repC fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:44|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica C Library 44 Library 44 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz fastq fastq 14506315716.0 48034158.0 BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665 151 151     3655344763 3770081597 3599601074 3480562617 725665 SRX23160972 SRS20111129 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01152 0.00012 0.00021 1e-05 0.99204 0.99963 0.40859 0.47368 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29221 29221 SRR27489738 SRX23160971 SRS20111128 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica C MPRA repC fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:43|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica C Library 43 Library 43 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz fastq fastq 14912162946.0 49378023.0 BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615 151 151     3752402181 3897191999 3682100517 3579734634 733615 SRX23160971 SRS20111128 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01301 0.0001 0.00023 0.0 0.99131 0.99963 0.41128 0.44444 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29222 29222 SRR27489739 SRX23160970 SRS20111127 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica C MPRA repC fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:42|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica C Library 42 Library 42 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz fastq fastq 16464627468.0 54518634.0 BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276 151 151     4169088631 4342123158 3994621055 3957976348 818276 SRX23160970 SRS20111127 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01689 8e-05 0.00051 0.0 0.99107 0.99973 0.40071 0.53846 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29223 29223 SRR27489740 SRX23160969 SRS20111125 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 6hpf replica C MPRA repC input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:41|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 6hpf replica C Library 41 Library 41 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz fastq fastq 10859083158.0 35957229.0 BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057 151 151     2762807814 2857106152 2613305234 2625327901 536057 SRX23160969 SRS20111125 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01753 0.0 0.00047 0.0 0.9907 1.0 0.40097   151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula 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
29229 29229 SRR27489746 SRX23160963 SRS20111121 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica C MPRA repC fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica C Library 36 Library 36 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz fastq fastq 13085558528.0 43329664.0 BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985 151 151     3305413622 3391845548 3249932870 3137708503 657985 SRX23160963 SRS20111121 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01098 8e-05 0.00025 0.0 0.99216 0.99973 0.4317 0.61538 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29230 29230 SRR27489747 SRX23160962 SRS20111119 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica C MPRA repC fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica C Library 35 Library 35 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz fastq fastq 16647721914.0 55124907.0 BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108 151 151     4231542934 4348688006 4050131444 4016534422 825108 SRX23160962 SRS20111119 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01514 0.00017 0.00035 3e-05 0.99109 0.99955 0.4372 0.30434 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29231 29231 SRR27489748 SRX23160961 SRS20111118 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica C MPRA repC fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica C Library 34 Library 34 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz fastq fastq 15431181052.0 51096626.0 BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999 151 151     3856018869 4036338306 3877988553 3660059325 775999 SRX23160961 SRS20111118 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01114 8e-05 0.00028 0.0 0.99192 0.99975 0.42956 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29232 29232 SRR27489749 SRX23160960 SRS20111117 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica C MPRA repC input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 2hpf replica C Library 33 Library 33 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz fastq fastq 11771229160.0 38977580.0 BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080 151 151     2999574420 3115525474 2806539264 2849003922 586080 SRX23160960 SRS20111117 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01997 2e-05 0.00054 0.0 0.99022 0.99993 0.41853 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29233 29233 SRR27489750 SRX23160959 SRS20111116 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica B MPRA repB fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:32|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica B Library 32 Library 32 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz fastq fastq 12683073766.0 41996933.0 BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624 151 151     3165850297 3286094227 3205853472 3024640146 635624 SRX23160959 SRS20111116 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00973 0.00093 0.00036 0.00015 0.99265 0.99819 0.4701 0.61111 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29234 29234 SRR27489751 SRX23160958 SRS20111115 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 10hpf replica B MPRA repB fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:31|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica B Library 31 Library 31 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz fastq fastq 11187950286.0 37046193.0 BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502 151 151     2805602272 2927866458 2773076846 2680845208 559502 SRX23160958 SRS20111115 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01142 0.0002 0.00018 2e-05 0.99243 0.99943 0.45894 0.54838 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29235 29235 SRR27489752 SRX23160957 SRS20111114 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica A MPRA repA fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica A Library 4 Library 4 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz fastq fastq 12108626278.0 40094789.0 BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268 151 151     3079403604 3149095123 2953175005 2926352278 600268 SRX23160957 SRS20111114 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.014 5e-05 0.00032 0.0 0.99137 0.99987 0.45127 0.28571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29236 29236 SRR27489753 SRX23160956 SRS20111113 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 10hpf replica B MPRA repB fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:30|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica B Library 30 Library 30 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz fastq fastq 15465851256.0 51211428.0 BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024 151 151     3889753740 4075740540 3791174754 3708409198 773024 SRX23160956 SRS20111113 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01609 0.00014 0.0003 3e-05 0.99139 0.99959 0.4335 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29237 29237 SRR27489754 SRX23160955 SRS20111112 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica B MPRA repB input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:29|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 10hpf replica B Library 29 Library 29 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz fastq fastq 12592035866.0 41695483.0 BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448 151 151     3220865280 3326103488 2978281202 3066156448 629448 SRX23160955 SRS20111112 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02168 1e-05 0.0006 0.0 0.98993 0.99997 0.41273 1.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29238 29238 SRR27489755 SRX23160954 SRS20111122 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica B MPRA repB fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:28|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica B Library 28 Library 28 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz fastq fastq 12606651156.0 41743878.0 BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136 151 151     3184687427 3283680489 3107570485 3030085619 627136 SRX23160954 SRS20111122 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01219 7e-05 0.00028 0.0 0.99182 0.99977 0.42217 0.45454 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29239 29239 SRR27489756 SRX23160953 SRS20111110 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica B MPRA repB fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:27|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica B Library 27 Library 27 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz fastq fastq 13738263880.0 45490940.0 BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066 151 151     3463772316 3608023656 3363805269 3301974573 688066 SRX23160953 SRS20111110 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01443 0.00014 0.00028 1e-05 0.99117 0.99957 0.38916 0.45833 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29240 29240 SRR27489757 SRX23160952 SRS20111111 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica B MPRA repB fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:26|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica B Library 26 Library 26 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz fastq fastq 10624262152.0 35179676.0 BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277 151 151     2680084455 2804915710 2592024460 2546707250 530277 SRX23160952 SRS20111111 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01636 0.00013 0.00046 0.0 0.99088 0.99959 0.39222 0.40909 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29241 29241 SRR27489758 SRX23160951 SRS20111109 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 6hpf replica B MPRA repB input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:25|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 6hpf replica B Library 25 Library 25 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz fastq fastq 10153888998.0 33622149.0 BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963 151 151     2587160061 2673241688 2432503358 2460478928 504963 SRX23160951 SRS20111109 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01911 2e-05 0.00061 0.0 0.99064 0.99995 0.42802 0.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula 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
29246 29246 SRR27489763 SRX23160946 SRS20111108 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica A MPRA repA fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica A Library 3 Library 3 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz fastq fastq 12524202136.0 41470868.0 BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842 151 151     3168466372 3269998328 3075956662 3009160932 619842 SRX23160946 SRS20111108 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01351 7e-05 0.00028 0.0 0.99168 0.99977 0.43472 0.54545 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29247 29247 SRR27489764 SRX23160945 SRS20111103 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica B MPRA repB fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica B Library 20 Library 20 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz fastq fastq 12514444214.0 41438557.0 BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303 151 151     3174354240 3246812350 3082021359 3010633962 622303 SRX23160945 SRS20111103 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01121 0.00016 0.00027 1e-05 0.99204 0.99953 0.43533 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29248 29248 SRR27489765 SRX23160944 SRS20111102 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica B MPRA repB fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica B Library 19 Library 19 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz fastq fastq 16535129670.0 54752085.0 BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421 151 151     4184643114 4312135767 4051628900 3985895468 826421 SRX23160944 SRS20111102 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01416 0.00017 0.00031 1e-05 0.9917 0.99941 0.40732 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29249 29249 SRR27489766 SRX23160943 SRS20111101 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica B MPRA repB fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica B Library 18 Library 18 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz fastq fastq 12692870042.0 42029371.0 BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284 151 151     3179006274 3325152682 3173386021 3014687781 637284 SRX23160943 SRS20111101 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01199 8e-05 0.0003 1e-05 0.99145 0.99979 0.40897 0.36363 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29250 29250 SRR27489767 SRX23160942 SRS20111100 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica B MPRA repB input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 2hpf replica B Library 17 Library 17 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz fastq fastq 13169436008.0 43607404.0 BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755 151 151     3341908647 3485072739 3171200836 3170595031 658755 SRX23160942 SRS20111100 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01868 5e-05 0.0006 0.0 0.99038 0.99983 0.41955 0.125 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29251 29251 SRR27489768 SRX23160941 SRS20111099 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica A MPRA repA fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:16|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica A Library 16 Library 16 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R2_001_MM_1.fastq.gz fastq fastq 13501095730.0 44705615.0 BSSE QGF 206651 HGWLYDSX3 3 MPRA repA fractions 8 9 10hpf CGGCGTGA GCGCCTGT S16 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3386778587;C:3499255836;G:3382745292;T:3231634315;N:681700 151 151     3386778587 3499255836 3382745292 3231634315 681700 SRX23160941 SRS20111099 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00829 0.00016 0.00011 0.0 0.99265 0.99949 0.49527 0.48275 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29252 29252 SRR27489769 SRX23160940 SRS20111096 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 10hpf replica A MPRA repA fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:15|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica A Library 15 Library 15 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R2_001_MM_1.fastq.gz fastq fastq 13046767232.0 43201216.0 BSSE QGF 206650 HGWLYDSX3 3 MPRA repA fractions 6 7 10hpf TAATACAG ATATTCAC S15 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3290688159;C:3400409529;G:3214905336;T:3140115501;N:648707 151 151     3290688159 3400409529 3214905336 3140115501 648707 SRX23160940 SRS20111096 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01093 0.0001 0.00011 0.0 0.99249 0.99967 0.43443 0.77777 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29253 29253 SRR27489770 SRX23160939 SRS20111097 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 10hpf replica A MPRA repA fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:14|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica A Library 14 Library 14 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R2_001_MM_1.fastq.gz fastq fastq 13986764580.0 46313790.0 BSSE QGF 206649 HGWLYDSX3 3 MPRA repA fractions 4 5 10hpf AATCCGGA CTACAGTT S14 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3536884918;C:3676313944;G:3410122661;T:3362749616;N:693441 151 151     3536884918 3676313944 3410122661 3362749616 693441 SRX23160939 SRS20111097 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01503 7e-05 0.00035 0.0 0.99141 0.99983 0.43326 0.77777 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29254 29254 SRR27489771 SRX23160938 SRS20111095 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica A MPRA repA input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:13|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 10hpf replica A Library 13 Library 13 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R2_001_MM_1.fastq.gz fastq fastq 11263507666.0 37296383.0 BSSE QGF 206648 HGWLYDSX3 3 MPRA repA input 10hpf GGCTTAAG TCGTGACC S13 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2881851385;C:2968960112;G:2663338223;T:2748794775;N:563171 151 151     2881851385 2968960112 2663338223 2748794775 563171 SRX23160938 SRS20111095 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02096 1e-05 0.00058 0.0 0.99022 0.99997 0.43837 1.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29255 29255 SRR27489772 SRX23160937 SRS20111098 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica A MPRA repA fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:12|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica A Library 12 Library 12 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz fastq fastq 14724761980.0 48757490.0 BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179 151 151     3711442998 3830334531 3642299006 3539948266 737179 SRX23160937 SRS20111098 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01161 8e-05 0.0002 1e-05 0.99214 0.99985 0.4529 0.3 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29256 29256 SRR27489773 SRX23160936 SRS20111094 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica A MPRA repA fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:11|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica A Library 11 Library 11 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R2_001_MM_1.fastq.gz fastq fastq 16713361312.0 55342256.0 BSSE QGF 206646 HGWLYDSX3 3 MPRA repA fractions 6 7 6hpf CCAAGTCT AAGGATGA S11 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4183339886;C:4365661507;G:4181177026;T:3982339731;N:843162 151 151     4183339886 4365661507 4181177026 3982339731 843162 SRX23160936 SRS20111094 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01132 0.00011 0.00024 0.0 0.99174 0.99965 0.40968 0.47368 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29257 29257 SRR27489774 SRX23160935 SRS20111093 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica A MPRA repA fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica A Library 2 Library 2 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz fastq fastq 16111078182.0 53347941.0 BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034 151 151     4069536779 4222816450 3957789955 3860129964 805034 SRX23160935 SRS20111093 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01511 5e-05 0.00034 0.0 0.99135 0.99985 0.41564 0.42857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29258 29258 SRR27489775 SRX23160934 SRS20111092 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica A MPRA repA input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 2hpf replica A Library 1 Library 1 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz fastq fastq 9769305890.0 32348695.0 BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485 151 151     2477269774 2598109179 2338444856 2354997596 484485 SRX23160934 SRS20111092 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0205 4e-05 0.00059 0.0 0.99013 0.99987 0.41957 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism 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");;