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
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,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,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,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
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
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,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,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,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,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
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,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