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31 rows where devstage_curation = "Gastrula" and experiment.library_selection = "RT-PCR"

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experiment.library_strategy 2

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RT-PCR · 31 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Gastrula · 31 ✖
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
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
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
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
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
47607 47607 SRR6996532 SRX3931184 SRS3164482 SRP137031 PRJNA432757 zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage PRJNA432757 Other To better understand the compensation network in MZmarcksb we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.       maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 2 marcksbMZ shield rep2   strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 2 MZmarcksb shield PE150 rep2 MZmarcksb shield PE150 rep2 The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1 g. The average final library size is 309 bp.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina MiSeq   SRP137031     marcksbMZ2_shield_R1.fastq.bz2 marcksbMZ2_shield_R2.fastq.bz2 fastq fastq 957075410.0 3388133.0 marcksbMZ2 shield R2.fastq.bz2 0:141.21 1:141.27 A:252634407;C:225426820;G:225127111;T:253882486;N:4586 141 141     252634407 225426820 225127111 253882486 4586 SRX3931184 SRS3164482 SRA688612 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences 2 0.9602 0.96488 0.04777 0.04815 0.76753 0.7697 0.48813 0.4867 150 151 B B biological fallback assumption illumina miseq unknown other trueseq bulk unknown unknown   China 2018-04-12 Gastrula Embryo Whole Organism All anatomical structures
47608 47608 SRR6996479 SRX3931150 SRS3164467 SRP137031 PRJNA432757 zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage PRJNA432757 Other To better understand the compensation network in MZmarcksb we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.       maternal zygotic mutant of marcksb whole embryos at shield stage from Danio rerio replicate 1 marcksbMZ shield rep1   strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: MZmarcksb embryos at shield stage replicate 1 MZmarcksb shield PE150 rep1 MZmarcksb shield PE150 rep1 The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1 g. The average final library size is 309 bp.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina MiSeq   SRP137031     marcksbMZ1_shield_R2.fastq.bz2 marcksbMZ1_shield_R1.fastq.bz2 fastq fastq 1298313857.0 4880467.0 marcksbMZ1 shield R2.fastq.bz2 0:132.94 1:133.09 A:343658239;C:305189492;G:304679186;T:344779644;N:7296 132 133     343658239 305189492 304679186 344779644 7296 SRX3931150 SRS3164467 SRA688589 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences 2 0.95673 0.96117 0.05347 0.05421 0.76751 0.76936 0.48125 0.48179 130 130 B B biological fallback assumption illumina miseq unknown other trueseq bulk unknown unknown   China 2018-04-12 Gastrula Embryo Whole Organism All anatomical structures
47609 47609 SRR6987273 SRX3926781 SRS3160495 SRP137031 PRJNA432757 zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage PRJNA432757 Other To better understand the compensation network in MZmarcksb we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.       WT whole embryos at shield stage from Danio rerio WT1 shield   strain:AB|dev stage:shield|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT embryos at shield stage replicate 2 wt shield PE rep2 wt shield PE rep2 The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1 g. The average final library size is 309 bp.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina MiSeq   SRP137031     WT2_shield_R1.fastq.bz2 WT2_shield_R2.fastq.bz2 fastq fastq 1076081986.0 3852554.0 WT2 shield R1.fastq.bz2 0:139.62 1:139.70 A:280164367;C:257377429;G:257794541;T:280730273;N:15376 139 139     280164367 257377429 257794541 280730273 15376 SRX3926781 SRS3160495 SRA687978 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93567 0.94244 0.04042 0.04049 0.77455 0.77697 0.48487 0.47998 151 151 B B biological fallback assumption illumina miseq unknown other trueseq bulk unknown unknown   China 2018-04-12 Gastrula Embryo Whole Organism All anatomical structures
47610 47610 SRR6933827 SRX3878878 SRS3118690 SRP137031 PRJNA432757 zebrafish Transcriptome on embryo of WT and MZmarcksb at shield stage PRJNA432757 Other To better understand the compensation network in MZmarcksb we carried out RNA seq analysis of the MZmarcksb mutants at shield stage.         WT1 shield rep1   strain:AB|dev stage:shield stage|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT embryos at shield stage replicate 1 wt shield PE rep1 wt shield PE rep1 The RNA was extracted using Trizol according to the manufacturer s manual. Then the RNA was purified using RNA purification kit Tiangen China. The RNA samples were quantified and integrity was assessed by the Agilent 2100 Bioanalyser. The RNA integrity Numbers RIN of all RNA samples were >8.0. The RNA libraries were prepared using the Illumina TruSeq RNA sample preparation kit v2. The amount of input RNA is 1 g. The average final library size is 309 bp.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA NextSeq 500   SRP137031     WT1_shield_R1.fastq.bz2 WT1_shield_R2.fastq.bz2 fastq fastq 892273276.0 3407597.0 WT1 shield R1.fastq.bz2 0:130.75 1:131.10 A:235694986;C:210056075;G:210344332;T:236174033;N:3850 130 131     235694986 210056075 210344332 236174033 3850 SRX3878878 SRS3118690 SRA681078 Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio Institute of Hydrobiology, Chinese Academy of Sciences 2 0.95143 0.95581 0.04389 0.04405 0.77143 0.77319 0.48336 0.48263 118 118 B B biological fallback assumption illumina nextseq unknown other trueseq bulk unknown unknown   China 2018-04-03 Gastrula Embryo Whole Organism All anatomical structures
51069 51069 SRR8926593 SRX5707650 SRS4646935 SRP192957 PRJNA515990 zebrafish miR 430 KO transcriptome PRJNA515990 Other MiR 430 is considered an important regulator during embryonic development but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement germ layer specification axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets we collected the WT miR 430 / and rescued embryos at shield stage and performed transcriptome sequencing.     miR 430 / embryos were injected with miR 430 rescued 20 embryos at shield stage were collected for RNA seq analsysis Rescued R6   strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:Rescued by miR 430 injection|BioSampleModel:Model organism or animal                 RNA seq of zebrafish miR 430 KO 5065335 5065335 high throughtput sequencing     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP192957     R6_GTGGCC_L001_R1_001.fastq.gz R6_GTGGCC_L001_R2_001.fastq.gz R6_GTGGCC_L002_R1_001.fastq.gz R6_GTGGCC_L002_R2_001.fastq.gz fastq fastq fastq fastq 3784504800.0 18922524.0 R6 GTGGCC L001 R1 001.fastq.gz 0:100 1:100 A:998174818;C:911994688;G:866970560;T:1007223918;N:140816 100 100     998174818 911994688 866970560 1007223918 140816 SRX5707650 SRS4646935 SRA876443 Sun Yat-Sen University|School of Life Sciences Sun Yat-Sen University 2 0.95548 0.95511 0.07794 0.079 0.75603 0.75933 0.48812 0.48112 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-04-18 Gastrula Embryo Whole Organism All anatomical structures
51070 51070 SRR8926594 SRX5707649 SRS4646934 SRP192957 PRJNA515990 zebrafish miR 430 KO transcriptome PRJNA515990 Other MiR 430 is considered an important regulator during embryonic development but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement germ layer specification axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets we collected the WT miR 430 / and rescued embryos at shield stage and performed transcriptome sequencing.     20 miR 430 / embryos at shield stage were collected for RNA seq analsysis MiR 430 / M6   strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:MiR 430 / |sample type:embryos|treatment:miR 430 was deleted by TALENs|BioSampleModel:Model organism or animal                 RNA seq of zebrafish miR 430 KO 5065334 5065334 high throughtput sequencing     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP192957     M6_GTGAAA_L002_R2_001.fastq.gz M6_GTGAAA_L002_R1_001.fastq.gz M6_GTGAAA_L001_R2_001.fastq.gz M6_GTGAAA_L001_R1_001.fastq.gz fastq fastq fastq fastq 3957356200.0 19786781.0 M6 GTGAAA L001 R1 001.fastq.gz 0:100 1:100 A:1047013756;C:951740713;G:905354408;T:1053098995;N:148328 100 100     1047013756 951740713 905354408 1053098995 148328 SRX5707649 SRS4646934 SRA876443 Sun Yat-Sen University|School of Life Sciences Sun Yat-Sen University 2 0.9588 0.95721 0.07699 0.07822 0.75422 0.75903 0.47996 0.48477 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-04-18 Gastrula Embryo Whole Organism All anatomical structures
51071 51071 SRR8926595 SRX5707648 SRS4646933 SRP192957 PRJNA515990 zebrafish miR 430 KO transcriptome PRJNA515990 Other MiR 430 is considered an important regulator during embryonic development but genetic loss of function study is still lacking. Here we demonstrated that genetic deletion of the miR 430 cluster resulted in developmental defects in cell movement germ layer specification axis patterning and organ progenitor formation in zebrafish. To identify miR 430 targets we collected the WT miR 430 / and rescued embryos at shield stage and performed transcriptome sequencing.     20 WT embryos at shield stage were collected for RNA seq analsysis WT W6   strain:AB|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:Hong Kong|age:6 hpf stage:shield stage|sex:pooled male and female|tissue:embyos|phenotype:WT|sample type:embryos|treatment:Control|BioSampleModel:Model organism or animal                 RNA seq of zebrafish miR 430 KO 5065333 5065333 high throughtput sequencing     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP192957     W6_GTCCGC_L001_R2_001.fastq.gz W6_GTCCGC_L002_R1_001.fastq.gz W6_GTCCGC_L002_R2_001.fastq.gz W6_GTCCGC_L001_R1_001.fastq.gz fastq fastq fastq fastq 3409986400.0 17049932.0 W6 GTCCGC L001 R1 001.fastq.gz 0:100 1:100 A:898095172;C:823280875;G:782808699;T:905676163;N:125491 100 100     898095172 823280875 782808699 905676163 125491 SRX5707648 SRS4646933 SRA876443 Sun Yat-Sen University|School of Life Sciences Sun Yat-Sen University 2 0.95598 0.95417 0.07794 0.07924 0.76063 0.7627 0.47632 0.47729 100 100 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-04-18 Gastrula 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");;