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run_metadata

88 rows where experiment.library_selection = "RT-PCR", experiment.platform = "ILLUMINA" and tissue_curation = "Whole Organism"

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devstage_curation 7

devstage_curation_coarse 4

technology 2

experiment.library_strategy 2

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 88 ✖

experiment.platform 1

  • ILLUMINA · 88 ✖

experiment.library_selection 1

  • RT-PCR · 88 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
29210 29210 SRR27489726 SRX23160983 SRS20111140 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica A MPRA repA fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:10|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica A Library 10 Library 10 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206645_HGWLYDSX3_3_MPRA_repA_fractions_4_5_6hpf_CTCTCGTC_TATAACCT_S10_L003_R2_001_MM_1.fastq.gz fastq fastq 13762167482.0 45570091.0 BSSE QGF 206645 HGWLYDSX3 3 MPRA repA fractions 4 5 6hpf CTCTCGTC TATAACCT S10 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3449173111;C:3620318973;G:3412595233;T:3279391764;N:688401 151 151     3449173111 3620318973 3412595233 3279391764 688401 SRX23160983 SRS20111140 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01348 9e-05 0.00033 1e-05 0.99151 0.99973 0.41104 0.57142 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29211 29211 SRR27489727 SRX23160982 SRS20111139 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 6hpf replica A MPRA repA input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:9|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 6hpf replica A Library 9 Library 9 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206644_HGWLYDSX3_3_MPRA_repA_input_6hpf_TCTCTACT_CGCGGTTC_S9_L003_R1_001_MM_1.fastq.gz fastq fastq 13570263998.0 44934649.0 BSSE QGF 206644 HGWLYDSX3 3 MPRA repA input 6hpf TCTCTACT CGCGGTTC S9 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3444180060;C:3577051220;G:3264051077;T:3284343514;N:638127 151 151     3444180060 3577051220 3264051077 3284343514 638127 SRX23160982 SRS20111139 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01809 5e-05 0.00042 0.0 0.99013 0.99985 0.41794 0.57142 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29212 29212 SRR27489728 SRX23160981 SRS20111138 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 4hpf replica A MPRA repA fractions 8 9 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:8|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 4hpf replica A Library 8 Library 8 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206643_HGWLYDSX3_3_MPRA_repA_fractions_8_9_4hpf_GACCTGAA_TTGGTGAG_S8_L003_R1_001_MM_1.fastq.gz fastq fastq 12066108000.0 39954000.0 BSSE QGF 206643 HGWLYDSX3 3 MPRA repA fractions 8 9 4hpf GACCTGAA TTGGTGAG S8 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3060316371;C:3136678983;G:2965588104;T:2902920606;N:603936 151 151     3060316371 3136678983 2965588104 2902920606 603936 SRX23160981 SRS20111138 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01336 5e-05 0.00027 0.0 0.99143 0.99983 0.40418 0.125 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29213 29213 SRR27489729 SRX23160980 SRS20111142 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 4hpf replica A MPRA repA fractions 6 7 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:7|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 4hpf replica A Library 7 Library 7 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206642_HGWLYDSX3_3_MPRA_repA_fractions_6_7_4hpf_AGTTCAGG_CCAACAGA_S7_L003_R1_001_MM_1.fastq.gz fastq fastq 11998643314.0 39730607.0 BSSE QGF 206642 HGWLYDSX3 3 MPRA repA fractions 6 7 4hpf AGTTCAGG CCAACAGA S7 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3044270548;C:3145201016;G:2907229129;T:2901344613;N:598008 151 151     3044270548 3145201016 2907229129 2901344613 598008 SRX23160980 SRS20111142 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01631 0.00013 0.00035 1e-05 0.99101 0.99965 0.40542 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29214 29214 SRR27489730 SRX23160979 SRS20111137 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 4hpf replica A MPRA repA fractions 4 5 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:6|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 4hpf replica A Library 6 Library 6 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206641_HGWLYDSX3_3_MPRA_repA_fractions_4_5_4hpf_TGGATCGA_GTGCGATA_S6_L003_R2_001_MM_1.fastq.gz fastq fastq 12838157410.0 42510455.0 BSSE QGF 206641 HGWLYDSX3 3 MPRA repA fractions 4 5 4hpf TGGATCGA GTGCGATA S6 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3238698530;C:3377705608;G:3143460419;T:3077655243;N:637610 151 151     3238698530 3377705608 3143460419 3077655243 637610 SRX23160979 SRS20111137 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01549 3e-05 0.00042 1e-05 0.99097 0.99995 0.42138 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29216 29216 SRR27489733 SRX23160976 SRS20111134 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica C MPRA repC fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:48|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica C Library 48 Library 48 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206683_HGWLYDSX3_3_MPRA_repC_fractions_8_9_10hpf_CAACAATG_CTTCACGG_S48_L003_R2_001_MM_1.fastq.gz fastq fastq 16074911568.0 53228184.0 BSSE QGF 206683 HGWLYDSX3 3 MPRA repC fractions 8 9 10hpf CAACAATG CTTCACGG S48 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4029048727;C:4167204709;G:4036912991;T:3840941866;N:803275 151 151     4029048727 4167204709 4036912991 3840941866 803275 SRX23160976 SRS20111134 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00795 0.00021 0.00019 2e-05 0.99263 0.99935 0.45247 0.62857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29217 29217 SRR27489734 SRX23160975 SRS20111132 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 10hpf replica C MPRA repC fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:47|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica C Library 47 Library 47 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206682_HGWLYDSX3_3_MPRA_repC_fractions_6_7_10hpf_GGTGAACC_GCGTTGGA_S47_L003_R2_001_MM_1.fastq.gz fastq fastq 16211925948.0 53681874.0 BSSE QGF 206682 HGWLYDSX3 3 MPRA repC fractions 6 7 10hpf GGTGAACC GCGTTGGA S47 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4078470905;C:4239434649;G:4000426230;T:3892801664;N:792500 151 151     4078470905 4239434649 4000426230 3892801664 792500 SRX23160975 SRS20111132 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01232 0.00028 0.00027 5e-05 0.99166 0.99926 0.4522 0.61904 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29218 29218 SRR27489735 SRX23160974 SRS20111131 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 10hpf replica C MPRA repC fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:46|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica C Library 46 Library 46 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206681_HGWLYDSX3_3_MPRA_repC_fractions_4_5_10hpf_AACAGGTT_ATACCAAG_S46_L003_R2_001_MM_1.fastq.gz fastq fastq 18761117310.0 62122905.0 BSSE QGF 206681 HGWLYDSX3 3 MPRA repC fractions 4 5 10hpf AACAGGTT ATACCAAG S46 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4746221682;C:4940258209;G:4549993563;T:4523714877;N:928979 151 151     4746221682 4940258209 4549993563 4523714877 928979 SRX23160974 SRS20111131 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01785 0.0002 0.00043 3e-05 0.9908 0.99951 0.45866 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29219 29219 SRR27489736 SRX23160973 SRS20111130 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica C MPRA repC input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:45|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 10hpf replica C Library 45 Library 45 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206680_HGWLYDSX3_3_MPRA_repC_input_10hpf_GCGCTCTA_GCTCCGAC_S45_L003_R2_001_MM_1.fastq.gz fastq fastq 15148053334.0 50159117.0 BSSE QGF 206680 HGWLYDSX3 3 MPRA repC input 10hpf GCGCTCTA GCTCCGAC S45 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3877492548;C:4007711111;G:3560735163;T:3701356537;N:757975 151 151     3877492548 4007711111 3560735163 3701356537 757975 SRX23160973 SRS20111130 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02196 3e-05 0.00062 1e-05 0.98944 0.99993 0.4404 0.66666 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29220 29220 SRR27489737 SRX23160972 SRS20111129 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica C MPRA repC fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:44|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica C Library 44 Library 44 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206679_HGWLYDSX3_3_MPRA_repC_fractions_8_9_6hpf_ATATCTCG_ATCTTAGT_S44_L003_R1_001_MM_1.fastq.gz fastq fastq 14506315716.0 48034158.0 BSSE QGF 206679 HGWLYDSX3 3 MPRA repC fractions 8 9 6hpf ATATCTCG ATCTTAGT S44 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3655344763;C:3770081597;G:3599601074;T:3480562617;N:725665 151 151     3655344763 3770081597 3599601074 3480562617 725665 SRX23160972 SRS20111129 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01152 0.00012 0.00021 1e-05 0.99204 0.99963 0.40859 0.47368 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29221 29221 SRR27489738 SRX23160971 SRS20111128 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica C MPRA repC fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:43|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica C Library 43 Library 43 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206678_HGWLYDSX3_3_MPRA_repC_fractions_6_7_6hpf_ACCTTGGC_GGCCTCAT_S43_L003_R2_001_MM_1.fastq.gz fastq fastq 14912162946.0 49378023.0 BSSE QGF 206678 HGWLYDSX3 3 MPRA repC fractions 6 7 6hpf ACCTTGGC GGCCTCAT S43 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3752402181;C:3897191999;G:3682100517;T:3579734634;N:733615 151 151     3752402181 3897191999 3682100517 3579734634 733615 SRX23160971 SRS20111128 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01301 0.0001 0.00023 0.0 0.99131 0.99963 0.41128 0.44444 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29222 29222 SRR27489739 SRX23160970 SRS20111127 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica C MPRA repC fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:42|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica C Library 42 Library 42 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206677_HGWLYDSX3_3_MPRA_repC_fractions_4_5_6hpf_GTTCCAAT_AATTCTGC_S42_L003_R1_001_MM_1.fastq.gz fastq fastq 16464627468.0 54518634.0 BSSE QGF 206677 HGWLYDSX3 3 MPRA repC fractions 4 5 6hpf GTTCCAAT AATTCTGC S42 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4169088631;C:4342123158;G:3994621055;T:3957976348;N:818276 151 151     4169088631 4342123158 3994621055 3957976348 818276 SRX23160970 SRS20111127 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01689 8e-05 0.00051 0.0 0.99107 0.99973 0.40071 0.53846 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29223 29223 SRR27489740 SRX23160969 SRS20111125 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 6hpf replica C MPRA repC input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:41|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 6hpf replica C Library 41 Library 41 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206676_HGWLYDSX3_3_MPRA_repC_input_6hpf_GCAATGCA_GGAACGTT_S41_L003_R2_001_MM_1.fastq.gz fastq fastq 10859083158.0 35957229.0 BSSE QGF 206676 HGWLYDSX3 3 MPRA repC input 6hpf GCAATGCA GGAACGTT S41 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2762807814;C:2857106152;G:2613305234;T:2625327901;N:536057 151 151     2762807814 2857106152 2613305234 2625327901 536057 SRX23160969 SRS20111125 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01753 0.0 0.00047 0.0 0.9907 1.0 0.40097   151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29224 29224 SRR27489741 SRX23160968 SRS20111133 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 4hpf replica A MPRA repA input 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:5|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 4hpf replica A Library 5 Library 5 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206640_HGWLYDSX3_3_MPRA_repA_input_4hpf_CAAGCTAG_ACATAGCG_S5_L003_R2_001_MM_1.fastq.gz fastq fastq 13631534966.0 45137533.0 BSSE QGF 206640 HGWLYDSX3 3 MPRA repA input 4hpf CAAGCTAG ACATAGCG S5 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3486253250;C:3611078376;G:3219396920;T:3314128840;N:677580 151 151     3486253250 3611078376 3219396920 3314128840 677580 SRX23160968 SRS20111133 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02225 2e-05 0.00066 0.0 0.98975 0.99993 0.40257 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29225 29225 SRR27489742 SRX23160967 SRS20111126 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 4hpf replica C MPRA repC fractions 8 9 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:40|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 4hpf replica C Library 40 Library 40 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206675_HGWLYDSX3_3_MPRA_repC_fractions_8_9_4hpf_ATGGCATG_AAGGTACC_S40_L003_R2_001_MM_1.fastq.gz fastq fastq 16854209582.0 55808641.0 BSSE QGF 206675 HGWLYDSX3 3 MPRA repC fractions 8 9 4hpf ATGGCATG AAGGTACC S40 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4270727222;C:4383022813;G:4143081915;T:4056541855;N:835777 151 151     4270727222 4383022813 4143081915 4056541855 835777 SRX23160967 SRS20111126 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01329 0.00015 0.00029 2e-05 0.99141 0.99953 0.4263 0.47826 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29226 29226 SRR27489743 SRX23160966 SRS20111124 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 4hpf replica C MPRA repC fractions 6 7 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:39|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 4hpf replica C Library 39 Library 39 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206674_HGWLYDSX3_3_MPRA_repC_fractions_6_7_4hpf_GGAGCGTC_GTCCGTGC_S39_L003_R2_001_MM_1.fastq.gz fastq fastq 12146174844.0 40219122.0 BSSE QGF 206674 HGWLYDSX3 3 MPRA repC fractions 6 7 4hpf GGAGCGTC GTCCGTGC S39 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3060215849;C:3176615755;G:3002666854;T:2906066243;N:610143 151 151     3060215849 3176615755 3002666854 2906066243 610143 SRX23160966 SRS20111124 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01309 0.0002 0.00031 0.0 0.99164 0.99939 0.40018 0.57142 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29227 29227 SRR27489744 SRX23160965 SRS20111123 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 4hpf replica C MPRA repC fractions 4 5 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:38|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 4hpf replica C Library 38 Library 38 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206673_HGWLYDSX3_3_MPRA_repC_fractions_4_5_4hpf_AAGATACT_ACTTACAT_S38_L003_R1_001_MM_1.fastq.gz fastq fastq 14100203330.0 46689415.0 BSSE QGF 206673 HGWLYDSX3 3 MPRA repC fractions 4 5 4hpf AAGATACT ACTTACAT S38 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3544539088;C:3702795841;G:3493240125;T:3358929671;N:698605 151 151     3544539088 3702795841 3493240125 3358929671 698605 SRX23160965 SRS20111123 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01368 0.00016 0.00037 0.0 0.99107 0.99951 0.40864 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29228 29228 SRR27489745 SRX23160964 SRS20111120 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 4hpf replica C MPRA repC input 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:37|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 4hpf replica C Library 37 Library 37 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206672_HGWLYDSX3_3_MPRA_repC_input_4hpf_GCGCAAGC_TCACGCCG_S37_L003_R2_001_MM_1.fastq.gz fastq fastq 10925301792.0 36176496.0 BSSE QGF 206672 HGWLYDSX3 3 MPRA repC input 4hpf GCGCAAGC TCACGCCG S37 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2802490901;C:2878602103;G:2592316062;T:2651349641;N:543085 151 151     2802490901 2878602103 2592316062 2651349641 543085 SRX23160964 SRS20111120 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02108 3e-05 0.0006 0.0 0.98981 0.99991 0.42181 0.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29229 29229 SRR27489746 SRX23160963 SRS20111121 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica C MPRA repC fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:36|replicate:replicate C|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica C Library 36 Library 36 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206671_HGWLYDSX3_3_MPRA_repC_fractions_8_9_2hpf_ATATGGAT_CTGTATTA_S36_L003_R2_001_MM_1.fastq.gz fastq fastq 13085558528.0 43329664.0 BSSE QGF 206671 HGWLYDSX3 3 MPRA repC fractions 8 9 2hpf ATATGGAT CTGTATTA S36 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3305413622;C:3391845548;G:3249932870;T:3137708503;N:657985 151 151     3305413622 3391845548 3249932870 3137708503 657985 SRX23160963 SRS20111121 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01098 8e-05 0.00025 0.0 0.99216 0.99973 0.4317 0.61538 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29230 29230 SRR27489747 SRX23160962 SRS20111119 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica C MPRA repC fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:35|replicate:replicate C|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica C Library 35 Library 35 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206670_HGWLYDSX3_3_MPRA_repC_fractions_6_7_2hpf_CGGACAAC_TCCGGATT_S35_L003_R1_001_MM_1.fastq.gz fastq fastq 16647721914.0 55124907.0 BSSE QGF 206670 HGWLYDSX3 3 MPRA repC fractions 6 7 2hpf CGGACAAC TCCGGATT S35 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4231542934;C:4348688006;G:4050131444;T:4016534422;N:825108 151 151     4231542934 4348688006 4050131444 4016534422 825108 SRX23160962 SRS20111119 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01514 0.00017 0.00035 3e-05 0.99109 0.99955 0.4372 0.30434 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29231 29231 SRR27489748 SRX23160961 SRS20111118 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica C MPRA repC fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:34|replicate:replicate C|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica C Library 34 Library 34 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206669_HGWLYDSX3_3_MPRA_repC_fractions_4_5_2hpf_TAAGTGGT_CTTAAGCC_S34_L003_R2_001_MM_1.fastq.gz fastq fastq 15431181052.0 51096626.0 BSSE QGF 206669 HGWLYDSX3 3 MPRA repC fractions 4 5 2hpf TAAGTGGT CTTAAGCC S34 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3856018869;C:4036338306;G:3877988553;T:3660059325;N:775999 151 151     3856018869 4036338306 3877988553 3660059325 775999 SRX23160961 SRS20111118 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01114 8e-05 0.00028 0.0 0.99192 0.99975 0.42956 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29232 29232 SRR27489749 SRX23160960 SRS20111117 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica C MPRA repC input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:33|replicate:replicate C|BioSampleModel:Model organism or animal                 Total 2hpf replica C Library 33 Library 33 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206668_HGWLYDSX3_3_MPRA_repC_input_2hpf_CTACGACA_GAGTCCAA_S33_L003_R1_001_MM_1.fastq.gz fastq fastq 11771229160.0 38977580.0 BSSE QGF 206668 HGWLYDSX3 3 MPRA repC input 2hpf CTACGACA GAGTCCAA S33 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2999574420;C:3115525474;G:2806539264;T:2849003922;N:586080 151 151     2999574420 3115525474 2806539264 2849003922 586080 SRX23160960 SRS20111117 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01997 2e-05 0.00054 0.0 0.99022 0.99993 0.41853 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29233 29233 SRR27489750 SRX23160959 SRS20111116 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica B MPRA repB fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:32|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica B Library 32 Library 32 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206667_HGWLYDSX3_3_MPRA_repB_fractions_8_9_10hpf_TCGTAGTG_AGACTTGG_S32_L003_R2_001_MM_1.fastq.gz fastq fastq 12683073766.0 41996933.0 BSSE QGF 206667 HGWLYDSX3 3 MPRA repB fractions 8 9 10hpf TCGTAGTG AGACTTGG S32 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3165850297;C:3286094227;G:3205853472;T:3024640146;N:635624 151 151     3165850297 3286094227 3205853472 3024640146 635624 SRX23160959 SRS20111116 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00973 0.00093 0.00036 0.00015 0.99265 0.99819 0.4701 0.61111 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29234 29234 SRR27489751 SRX23160958 SRS20111115 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 10hpf replica B MPRA repB fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:31|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica B Library 31 Library 31 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206666_HGWLYDSX3_3_MPRA_repB_fractions_6_7_10hpf_GATTCTGC_GACGAGAG_S31_L003_R2_001_MM_1.fastq.gz fastq fastq 11187950286.0 37046193.0 BSSE QGF 206666 HGWLYDSX3 3 MPRA repB fractions 6 7 10hpf GATTCTGC GACGAGAG S31 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2805602272;C:2927866458;G:2773076846;T:2680845208;N:559502 151 151     2805602272 2927866458 2773076846 2680845208 559502 SRX23160958 SRS20111115 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01142 0.0002 0.00018 2e-05 0.99243 0.99943 0.45894 0.54838 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29235 29235 SRR27489752 SRX23160957 SRS20111114 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica A MPRA repA fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:4|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica A Library 4 Library 4 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206639_HGWLYDSX3_3_MPRA_repA_fractions_8_9_2hpf_GCTTGTCA_GAACATAC_S4_L003_R1_001_MM_1.fastq.gz fastq fastq 12108626278.0 40094789.0 BSSE QGF 206639 HGWLYDSX3 3 MPRA repA fractions 8 9 2hpf GCTTGTCA GAACATAC S4 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3079403604;C:3149095123;G:2953175005;T:2926352278;N:600268 151 151     3079403604 3149095123 2953175005 2926352278 600268 SRX23160957 SRS20111114 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.014 5e-05 0.00032 0.0 0.99137 0.99987 0.45127 0.28571 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29236 29236 SRR27489753 SRX23160956 SRS20111113 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 10hpf replica B MPRA repB fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:30|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica B Library 30 Library 30 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206665_HGWLYDSX3_3_MPRA_repB_fractions_4_5_10hpf_AGCCTCAT_AGTAGAGA_S30_L003_R2_001_MM_1.fastq.gz fastq fastq 15465851256.0 51211428.0 BSSE QGF 206665 HGWLYDSX3 3 MPRA repB fractions 4 5 10hpf AGCCTCAT AGTAGAGA S30 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3889753740;C:4075740540;G:3791174754;T:3708409198;N:773024 151 151     3889753740 4075740540 3791174754 3708409198 773024 SRX23160956 SRS20111113 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01609 0.00014 0.0003 3e-05 0.99139 0.99959 0.4335 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29237 29237 SRR27489754 SRX23160955 SRS20111112 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica B MPRA repB input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:29|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 10hpf replica B Library 29 Library 29 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206664_HGWLYDSX3_3_MPRA_repB_input_10hpf_CGTTAGAA_TTCAGGTC_S29_L003_R2_001_MM_1.fastq.gz fastq fastq 12592035866.0 41695483.0 BSSE QGF 206664 HGWLYDSX3 3 MPRA repB input 10hpf CGTTAGAA TTCAGGTC S29 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3220865280;C:3326103488;G:2978281202;T:3066156448;N:629448 151 151     3220865280 3326103488 2978281202 3066156448 629448 SRX23160955 SRS20111112 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02168 1e-05 0.0006 0.0 0.98993 0.99997 0.41273 1.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29238 29238 SRR27489755 SRX23160954 SRS20111122 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica B MPRA repB fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:28|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica B Library 28 Library 28 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206663_HGWLYDSX3_3_MPRA_repB_fractions_8_9_6hpf_TACCGAGG_CCTGAACT_S28_L003_R2_001_MM_1.fastq.gz fastq fastq 12606651156.0 41743878.0 BSSE QGF 206663 HGWLYDSX3 3 MPRA repB fractions 8 9 6hpf TACCGAGG CCTGAACT S28 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3184687427;C:3283680489;G:3107570485;T:3030085619;N:627136 151 151     3184687427 3283680489 3107570485 3030085619 627136 SRX23160954 SRS20111122 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01219 7e-05 0.00028 0.0 0.99182 0.99977 0.42217 0.45454 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29239 29239 SRR27489756 SRX23160953 SRS20111110 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica B MPRA repB fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:27|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica B Library 27 Library 27 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206662_HGWLYDSX3_3_MPRA_repB_fractions_6_7_6hpf_AATGCCTC_TCGATCCA_S27_L003_R1_001_MM_1.fastq.gz fastq fastq 13738263880.0 45490940.0 BSSE QGF 206662 HGWLYDSX3 3 MPRA repB fractions 6 7 6hpf AATGCCTC TCGATCCA S27 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3463772316;C:3608023656;G:3363805269;T:3301974573;N:688066 151 151     3463772316 3608023656 3363805269 3301974573 688066 SRX23160953 SRS20111110 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01443 0.00014 0.00028 1e-05 0.99117 0.99957 0.38916 0.45833 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29240 29240 SRR27489757 SRX23160952 SRS20111111 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 6hpf replica B MPRA repB fractions 4 5 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:26|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 6hpf replica B Library 26 Library 26 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206661_HGWLYDSX3_3_MPRA_repB_fractions_4_5_6hpf_GGCATTCT_CTAGCTTG_S26_L003_R1_001_MM_1.fastq.gz fastq fastq 10624262152.0 35179676.0 BSSE QGF 206661 HGWLYDSX3 3 MPRA repB fractions 4 5 6hpf GGCATTCT CTAGCTTG S26 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2680084455;C:2804915710;G:2592024460;T:2546707250;N:530277 151 151     2680084455 2804915710 2592024460 2546707250 530277 SRX23160952 SRS20111111 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01636 0.00013 0.00046 0.0 0.99088 0.99959 0.39222 0.40909 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29241 29241 SRR27489758 SRX23160951 SRS20111109 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 6hpf replica B MPRA repB input 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:25|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 6hpf replica B Library 25 Library 25 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206660_HGWLYDSX3_3_MPRA_repB_input_6hpf_TTACAGGA_TGACAAGC_S25_L003_R2_001_MM_1.fastq.gz fastq fastq 10153888998.0 33622149.0 BSSE QGF 206660 HGWLYDSX3 3 MPRA repB input 6hpf TTACAGGA TGACAAGC S25 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2587160061;C:2673241688;G:2432503358;T:2460478928;N:504963 151 151     2587160061 2673241688 2432503358 2460478928 504963 SRX23160951 SRS20111109 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01911 2e-05 0.00061 0.0 0.99064 0.99995 0.42802 0.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29242 29242 SRR27489759 SRX23160950 SRS20111107 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 4hpf replica B MPRA repB fractions 8 9 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:24|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 4hpf replica B Library 24 Library 24 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206659_HGWLYDSX3_3_MPRA_repB_fractions_8_9_4hpf_CCGTGAAG_CAGTGGAT_S24_L003_R2_001_MM_1.fastq.gz fastq fastq 11600767978.0 38413139.0 BSSE QGF 206659 HGWLYDSX3 3 MPRA repB fractions 8 9 4hpf CCGTGAAG CAGTGGAT S24 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2943303855;C:3024500200;G:2833306086;T:2799077405;N:580432 151 151     2943303855 3024500200 2833306086 2799077405 580432 SRX23160950 SRS20111107 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01371 0.00013 0.00031 1e-05 0.99143 0.99955 0.41912 0.5909 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29243 29243 SRR27489760 SRX23160949 SRS20111106 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 4hpf replica B MPRA repB fractions 6 7 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:23|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 4hpf replica B Library 23 Library 23 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206658_HGWLYDSX3_3_MPRA_repB_fractions_6_7_4hpf_CTTGGTAT_CCAAGTCC_S23_L003_R2_001_MM_1.fastq.gz fastq fastq 13216553444.0 43763422.0 BSSE QGF 206658 HGWLYDSX3 3 MPRA repB fractions 6 7 4hpf CTTGGTAT CCAAGTCC S23 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3339016083;C:3457419680;G:3233764657;T:3185687490;N:665534 151 151     3339016083 3457419680 3233764657 3185687490 665534 SRX23160949 SRS20111106 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01431 0.00024 0.00034 1e-05 0.99135 0.99924 0.41915 0.45238 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29244 29244 SRR27489761 SRX23160948 SRS20111105 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 4hpf replica B MPRA repB fractions 4 5 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:22|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 4hpf replica B Library 22 Library 22 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206657_HGWLYDSX3_3_MPRA_repB_fractions_4_5_4hpf_ATGAGGCC_GTTAATTG_S22_L003_R2_001_MM_1.fastq.gz fastq fastq 11938250562.0 39530631.0 BSSE QGF 206657 HGWLYDSX3 3 MPRA repB fractions 4 5 4hpf ATGAGGCC GTTAATTG S22 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3040684418;C:3144238599;G:2873359599;T:2879374531;N:593415 151 151     3040684418 3144238599 2873359599 2879374531 593415 SRX23160948 SRS20111105 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0185 8e-05 0.00056 0.0 0.9903 0.99969 0.4376 0.4 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29245 29245 SRR27489762 SRX23160947 SRS20111104 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 4hpf replica B MPRA repB input 4hpf   strain:TLAB|age:4 hpf|dev stage:sphere|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:21|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 4hpf replica B Library 21 Library 21 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206656_HGWLYDSX3_3_MPRA_repB_input_4hpf_GCAGAATT_ACCGGCCA_S21_L003_R1_001_MM_1.fastq.gz fastq fastq 14482326346.0 47954723.0 BSSE QGF 206656 HGWLYDSX3 3 MPRA repB input 4hpf GCAGAATT ACCGGCCA S21 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3697691325;C:3838972714;G:3432418300;T:3512522230;N:721777 151 151     3697691325 3838972714 3432418300 3512522230 721777 SRX23160947 SRS20111104 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0211 2e-05 0.00055 0.0 0.9903 0.99993 0.42543 0.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Blastula Embryo Whole Organism All anatomical structures
29246 29246 SRR27489763 SRX23160946 SRS20111108 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica A MPRA repA fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:3|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica A Library 3 Library 3 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206638_HGWLYDSX3_3_MPRA_repA_fractions_6_7_2hpf_ATCCACTG_AGGTGCGT_S3_L003_R1_001_MM_1.fastq.gz fastq fastq 12524202136.0 41470868.0 BSSE QGF 206638 HGWLYDSX3 3 MPRA repA fractions 6 7 2hpf ATCCACTG AGGTGCGT S3 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3168466372;C:3269998328;G:3075956662;T:3009160932;N:619842 151 151     3168466372 3269998328 3075956662 3009160932 619842 SRX23160946 SRS20111108 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01351 7e-05 0.00028 0.0 0.99168 0.99977 0.43472 0.54545 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29247 29247 SRR27489764 SRX23160945 SRS20111103 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 2hpf replica B MPRA repB fractions 8 9 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:20|replicate:replicate B|BioSampleModel:Model organism or animal                 HMW fraction 2hpf replica B Library 20 Library 20 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206655_HGWLYDSX3_3_MPRA_repB_fractions_8_9_2hpf_AACGTTCC_GGAGTACT_S20_L003_R2_001_MM_1.fastq.gz fastq fastq 12514444214.0 41438557.0 BSSE QGF 206655 HGWLYDSX3 3 MPRA repB fractions 8 9 2hpf AACGTTCC GGAGTACT S20 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3174354240;C:3246812350;G:3082021359;T:3010633962;N:622303 151 151     3174354240 3246812350 3082021359 3010633962 622303 SRX23160945 SRS20111103 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01121 0.00016 0.00027 1e-05 0.99204 0.99953 0.43533 0.5 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29248 29248 SRR27489765 SRX23160944 SRS20111102 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 2hpf replica B MPRA repB fractions 6 7 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:19|replicate:replicate B|BioSampleModel:Model organism or animal                 LMW fraction 2hpf replica B Library 19 Library 19 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R2_001_MM_1.fastq.gz BSSE_QGF_206654_HGWLYDSX3_3_MPRA_repB_fractions_6_7_2hpf_GGTACCTT_AAGACGTC_S19_L003_R1_001_MM_1.fastq.gz fastq fastq 16535129670.0 54752085.0 BSSE QGF 206654 HGWLYDSX3 3 MPRA repB fractions 6 7 2hpf GGTACCTT AAGACGTC S19 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4184643114;C:4312135767;G:4051628900;T:3985895468;N:826421 151 151     4184643114 4312135767 4051628900 3985895468 826421 SRX23160944 SRS20111102 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01416 0.00017 0.00031 1e-05 0.9917 0.99941 0.40732 0.6 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29249 29249 SRR27489766 SRX23160943 SRS20111101 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica B MPRA repB fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:18|replicate:replicate B|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica B Library 18 Library 18 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206653_HGWLYDSX3_3_MPRA_repB_fractions_4_5_2hpf_GCACGGAC_GTCTCGCA_S18_L003_R2_001_MM_1.fastq.gz fastq fastq 12692870042.0 42029371.0 BSSE QGF 206653 HGWLYDSX3 3 MPRA repB fractions 4 5 2hpf GCACGGAC GTCTCGCA S18 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3179006274;C:3325152682;G:3173386021;T:3014687781;N:637284 151 151     3179006274 3325152682 3173386021 3014687781 637284 SRX23160943 SRS20111101 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01199 8e-05 0.0003 1e-05 0.99145 0.99979 0.40897 0.36363 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29250 29250 SRR27489767 SRX23160942 SRS20111100 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica B MPRA repB input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:17|replicate:replicate B|BioSampleModel:Model organism or animal                 Total 2hpf replica B Library 17 Library 17 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206652_HGWLYDSX3_3_MPRA_repB_input_2hpf_ATGTAAGT_ACTCTATG_S17_L003_R2_001_MM_1.fastq.gz fastq fastq 13169436008.0 43607404.0 BSSE QGF 206652 HGWLYDSX3 3 MPRA repB input 2hpf ATGTAAGT ACTCTATG S17 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3341908647;C:3485072739;G:3171200836;T:3170595031;N:658755 151 151     3341908647 3485072739 3171200836 3170595031 658755 SRX23160942 SRS20111100 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01868 5e-05 0.0006 0.0 0.99038 0.99983 0.41955 0.125 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29251 29251 SRR27489768 SRX23160941 SRS20111099 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 10hpf replica A MPRA repA fractions 8 9 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:16|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 10hpf replica A Library 16 Library 16 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206651_HGWLYDSX3_3_MPRA_repA_fractions_8_9_10hpf_CGGCGTGA_GCGCCTGT_S16_L003_R2_001_MM_1.fastq.gz fastq fastq 13501095730.0 44705615.0 BSSE QGF 206651 HGWLYDSX3 3 MPRA repA fractions 8 9 10hpf CGGCGTGA GCGCCTGT S16 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3386778587;C:3499255836;G:3382745292;T:3231634315;N:681700 151 151     3386778587 3499255836 3382745292 3231634315 681700 SRX23160941 SRS20111099 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.00829 0.00016 0.00011 0.0 0.99265 0.99949 0.49527 0.48275 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29252 29252 SRR27489769 SRX23160940 SRS20111096 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 10hpf replica A MPRA repA fractions 6 7 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:15|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 10hpf replica A Library 15 Library 15 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206650_HGWLYDSX3_3_MPRA_repA_fractions_6_7_10hpf_TAATACAG_ATATTCAC_S15_L003_R2_001_MM_1.fastq.gz fastq fastq 13046767232.0 43201216.0 BSSE QGF 206650 HGWLYDSX3 3 MPRA repA fractions 6 7 10hpf TAATACAG ATATTCAC S15 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3290688159;C:3400409529;G:3214905336;T:3140115501;N:648707 151 151     3290688159 3400409529 3214905336 3140115501 648707 SRX23160940 SRS20111096 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01093 0.0001 0.00011 0.0 0.99249 0.99967 0.43443 0.77777 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29253 29253 SRR27489770 SRX23160939 SRS20111097 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 10hpf replica A MPRA repA fractions 4 5 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:14|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 10hpf replica A Library 14 Library 14 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206649_HGWLYDSX3_3_MPRA_repA_fractions_4_5_10hpf_AATCCGGA_CTACAGTT_S14_L003_R2_001_MM_1.fastq.gz fastq fastq 13986764580.0 46313790.0 BSSE QGF 206649 HGWLYDSX3 3 MPRA repA fractions 4 5 10hpf AATCCGGA CTACAGTT S14 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3536884918;C:3676313944;G:3410122661;T:3362749616;N:693441 151 151     3536884918 3676313944 3410122661 3362749616 693441 SRX23160939 SRS20111097 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01503 7e-05 0.00035 0.0 0.99141 0.99983 0.43326 0.77777 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29254 29254 SRR27489771 SRX23160938 SRS20111095 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 10hpf replica A MPRA repA input 10hpf   strain:TLAB|age:10 hpf|dev stage:bud|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:13|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 10hpf replica A Library 13 Library 13 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206648_HGWLYDSX3_3_MPRA_repA_input_10hpf_GGCTTAAG_TCGTGACC_S13_L003_R2_001_MM_1.fastq.gz fastq fastq 11263507666.0 37296383.0 BSSE QGF 206648 HGWLYDSX3 3 MPRA repA input 10hpf GGCTTAAG TCGTGACC S13 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2881851385;C:2968960112;G:2663338223;T:2748794775;N:563171 151 151     2881851385 2968960112 2663338223 2748794775 563171 SRX23160938 SRS20111095 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.02096 1e-05 0.00058 0.0 0.99022 0.99997 0.43837 1.0 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29255 29255 SRR27489772 SRX23160937 SRS20111098 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction HMW fraction 6hpf replica A MPRA repA fractions 8 9 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:12|replicate:replicate A|BioSampleModel:Model organism or animal                 HMW fraction 6hpf replica A Library 12 Library 12 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206647_HGWLYDSX3_3_MPRA_repA_fractions_8_9_6hpf_TTGGACTC_GGAAGCAG_S12_L003_R2_001_MM_1.fastq.gz fastq fastq 14724761980.0 48757490.0 BSSE QGF 206647 HGWLYDSX3 3 MPRA repA fractions 8 9 6hpf TTGGACTC GGAAGCAG S12 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:3711442998;C:3830334531;G:3642299006;T:3539948266;N:737179 151 151     3711442998 3830334531 3642299006 3539948266 737179 SRX23160937 SRS20111098 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01161 8e-05 0.0002 1e-05 0.99214 0.99985 0.4529 0.3 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29256 29256 SRR27489773 SRX23160936 SRS20111094 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction LMW fraction 6hpf replica A MPRA repA fractions 6 7 6hpf   strain:TLAB|age:6 hpf|dev stage:shield|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:11|replicate:replicate A|BioSampleModel:Model organism or animal                 LMW fraction 6hpf replica A Library 11 Library 11 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206646_HGWLYDSX3_3_MPRA_repA_fractions_6_7_6hpf_CCAAGTCT_AAGGATGA_S11_L003_R2_001_MM_1.fastq.gz fastq fastq 16713361312.0 55342256.0 BSSE QGF 206646 HGWLYDSX3 3 MPRA repA fractions 6 7 6hpf CCAAGTCT AAGGATGA S11 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4183339886;C:4365661507;G:4181177026;T:3982339731;N:843162 151 151     4183339886 4365661507 4181177026 3982339731 843162 SRX23160936 SRS20111094 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01132 0.00011 0.00024 0.0 0.99174 0.99965 0.40968 0.47368 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Gastrula Embryo Whole Organism All anatomical structures
29257 29257 SRR27489774 SRX23160935 SRS20111093 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     polysome fraction 80S fraction 2hpf replica A MPRA repA fractions 4 5 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:2|replicate:replicate A|BioSampleModel:Model organism or animal                 80S fraction 2hpf replica A Library 2 Library 2 Total RNA was extracted from polysome fractionated sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206637_HGWLYDSX3_3_MPRA_repA_fractions_4_5_2hpf_TTGGACTT_TATGAGTA_S2_L003_R2_001_MM_1.fastq.gz fastq fastq 16111078182.0 53347941.0 BSSE QGF 206637 HGWLYDSX3 3 MPRA repA fractions 4 5 2hpf TTGGACTT TATGAGTA S2 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:4069536779;C:4222816450;G:3957789955;T:3860129964;N:805034 151 151     4069536779 4222816450 3957789955 3860129964 805034 SRX23160935 SRS20111093 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.01511 5e-05 0.00034 0.0 0.99135 0.99985 0.41564 0.42857 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
29258 29258 SRR27489775 SRX23160934 SRS20111092 SRP483112 PRJNA1056276 five prime UTR MPRA during early zebrafish embryogenesis PRJNA1056276 Other The goal is to determine the contribution of zebrafish five prime UTR sequences to translation initiation. The five prime UTR MPRA reporter library was injected at the 1 cell stage and samples were collected during early stages of embryogenesis. Polysome profiling was performed to quantify ribosome occupancy of each five prime UTR reporter.     input sample Total 2hpf replica A MPRA repA input 2hpf   strain:TLAB|age:2 hpf|dev stage:64 cells|collection date:2022 05 16|geo loc name:Switzerland: Basel|sex:not applicable|tissue:whole embryo|biomaterial provider:Schier lab|collected by:Madalena M. Reimao Pinto|genotype:WT|growth protocol:E3 buffer standard conditions|sample type:100 embryos|sample number:1|replicate:replicate A|BioSampleModel:Model organism or animal                 Total 2hpf replica A Library 1 Library 1 Total RNA was extracted from input sample RT was performed with reporter specific primer UMI were introduced ath the five primeend and library was amplified to include adapters compatible with Illumina sequencing.     OTHER TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP483112     BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R1_001_MM_1.fastq.gz BSSE_QGF_206636_HGWLYDSX3_3_MPRA_repA_input_2hpf_GGACTTGG_CGCAGACG_S1_L003_R2_001_MM_1.fastq.gz fastq fastq 9769305890.0 32348695.0 BSSE QGF 206636 HGWLYDSX3 3 MPRA repA input 2hpf GGACTTGG CGCAGACG S1 L003 R1 001 MM 1.fastq.gz 0:151 1:151 A:2477269774;C:2598109179;G:2338444856;T:2354997596;N:484485 151 151     2477269774 2598109179 2338444856 2354997596 484485 SRX23160934 SRS20111092 SRA1775336 University of Basel|Biozentrum Basel University of Basel 2 0.0205 4e-05 0.00059 0.0 0.99013 0.99987 0.41957 0.33333 151 151 T T mates < 9% mapping rate illumina novaseq_era 5prime other unknown bulk unknown unknown   Switzerland 2024-01-11 Cleavage Embryo Whole Organism All anatomical structures
31884 31884 SRR28747851 SRX24313483 SRS21075233 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 3 Ctrl 3 Ctrl 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-3_S26_L004_R2_001.fastq.gz Ctrl-3_S26_L004_R1_001.fastq.gz fastq fastq 6658139400.0 22193798.0 Ctrl 3 S26 L004 R1 001.fastq.gz 0:150 1:150 A:1953050910;C:1380426193;G:1413459206;T:1911166654;N:36437 150 150     1953050910 1380426193 1413459206 1911166654 36437 SRX24313483 SRS21075233 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94694 0.94695 0.14305 0.14206 0.70412 0.70473 0.59878 0.59922 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31885 31885 SRR28747852 SRX24313482 SRS21075231 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 2 Ctrl 2 Ctrl 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-2_S25_L004_R1_001.fastq.gz Ctrl-2_S25_L004_R2_001.fastq.gz fastq fastq 7515161100.0 25050537.0 Ctrl 2 S25 L004 R1 001.fastq.gz 0:150 1:150 A:2218032458;C:1545198589;G:1580900913;T:2170988635;N:40505 150 150     2218032458 1545198589 1580900913 2170988635 40505 SRX24313482 SRS21075231 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94205 0.94032 0.15138 0.15085 0.69578 0.69645 0.5641 0.56481 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31886 31886 SRR28747853 SRX24313481 SRS21075234 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 1 Ctrl 1 Ctrl 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-1_S24_L004_R1_001.fastq.gz Ctrl-1_S24_L004_R2_001.fastq.gz fastq fastq 9747041100.0 32490137.0 Ctrl 1 S24 L004 R1 001.fastq.gz 0:150 1:150 A:2863031605;C:2014131410;G:2067943208;T:2801881561;N:53316 150 150     2863031605 2014131410 2067943208 2801881561 53316 SRX24313481 SRS21075234 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94378 0.94419 0.14935 0.14934 0.70749 0.7069 0.60161 0.59912 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31887 31887 SRR28747854 SRX24313480 SRS21075232 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 3 4OI 3 4OI 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-3_S23_L004_R1_001.fastq.gz 4OI-3_S23_L004_R2_001.fastq.gz fastq fastq 8273990400.0 27579968.0 4OI 3 S23 L004 R1 001.fastq.gz 0:150 1:150 A:2162937415;C:1975194532;G:2012089890;T:2123723196;N:45367 150 150     2162937415 1975194532 2012089890 2123723196 45367 SRX24313480 SRS21075232 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96535 0.96542 0.03083 0.03097 0.71279 0.71295 0.48276 0.47927 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31888 31888 SRR28747855 SRX24313479 SRS21075230 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 2 4OI 2 4OI 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-2_S28_L003_R1_001.fastq.gz 4OI-2_S28_L003_R2_001.fastq.gz fastq fastq 6579714300.0 21932381.0 4OI 2 S28 L003 R1 001.fastq.gz 0:150 1:150 A:1710345718;C:1580260893;G:1608081826;T:1680921918;N:103945 150 150     1710345718 1580260893 1608081826 1680921918 103945 SRX24313479 SRS21075230 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96511 0.96418 0.03843 0.0384 0.70179 0.7027 0.49174 0.5066 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31889 31889 SRR28747856 SRX24313478 SRS21075229 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 1 4OI 1 4OI 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-1_S27_L003_R1_001.fastq.gz 4OI-1_S27_L003_R2_001.fastq.gz fastq fastq 7099570500.0 23665235.0 4OI 1 S27 L003 R1 001.fastq.gz 0:150 1:150 A:1858012411;C:1693592911;G:1723374425;T:1824476953;N:113800 150 150     1858012411 1693592911 1723374425 1824476953 113800 SRX24313478 SRS21075229 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96619 0.96559 0.04154 0.04152 0.70386 0.70412 0.48321 0.49372 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
32617 32617 SRR29366294 SRX24880743 SRS21589520 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs4   strain:TU|isolate:NPs4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs4 NPs4 A total amount of 9 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0022_good_1.fq.gz Unknown_BO623-04T0022_good_2.fq.gz fastq fastq 6748273836.0 22592809.0 Unknown BO623 04T0022 good 1.fq.gz 0:149.35 1:149.35 A:1774719919;C:1597377190;G:1614927098;T:1761071358;N:178271 149 149     1774719919 1597377190 1614927098 1761071358 178271 SRX24880743 SRS21589520 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32618 32618 SRR29366295 SRX24880742 SRS21589518 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs3   strain:TU|isolate:NPs3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs3 NPs3 A total amount of 8 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0021_good_1.fq.gz Unknown_BO623-04T0021_good_2.fq.gz fastq fastq 6529485490.0 21847936.0 Unknown BO623 04T0021 good 1.fq.gz 0:149.43 1:149.43 A:1717039978;C:1547743896;G:1563982349;T:1700522682;N:196585 149 149     1717039978 1547743896 1563982349 1700522682 196585 SRX24880742 SRS21589518 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32619 32619 SRR29366296 SRX24880741 SRS21589519 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs2   strain:TU|isolate:NPs2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs2 NPs2 A total amount of 7 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0020_good_1.fq.gz Unknown_BO623-04T0020_good_2.fq.gz fastq fastq 6699049910.0 22407080.0 Unknown BO623 04T0020 good 1.fq.gz 0:149.49 1:149.49 A:1761959579;C:1586799482;G:1603631340;T:1746520369;N:139140 149 149     1761959579 1586799482 1603631340 1746520369 139140 SRX24880741 SRS21589519 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32620 32620 SRR29366297 SRX24880740 SRS21589517 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs1   strain:TU|isolate:NPs1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs1 NPs1 A total amount of 6 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0019_good_1.fq.gz Unknown_BO623-04T0019_good_2.fq.gz fastq fastq 6132468788.0 20516184.0 Unknown BO623 04T0019 good 1.fq.gz 0:149.45 1:149.45 A:1607332987;C:1458658424;G:1471957341;T:1594421337;N:98699 149 149     1607332987 1458658424 1471957341 1594421337 98699 SRX24880740 SRS21589517 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32621 32621 SRR29366298 SRX24880739 SRS21589516 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C6   strain:TU|isolate:Control6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C6 C6 A total amount of 5 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0018_good_1.fq.gz Unknown_BO623-04T0018_good_2.fq.gz fastq fastq 5940082248.0 19857041.0 Unknown BO623 04T0018 good 1.fq.gz 0:149.57 1:149.57 A:1533707674;C:1435538751;G:1452812826;T:1517833025;N:189972 149 149     1533707674 1435538751 1452812826 1517833025 189972 SRX24880739 SRS21589516 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32622 32622 SRR29366299 SRX24880738 SRS21589515 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C5   strain:TU|isolate:Control5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C5 C5 A total amount of 4 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0017_good_1.fq.gz Unknown_BO623-04T0017_good_2.fq.gz fastq fastq 6758002932.0 22599590.0 Unknown BO623 04T0017 good 1.fq.gz 0:149.52 1:149.52 A:1739766340;C:1637642157;G:1652002401;T:1728330255;N:261779 149 149     1739766340 1637642157 1652002401 1728330255 261779 SRX24880738 SRS21589515 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32623 32623 SRR29366300 SRX24880737 SRS21589514 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C4   strain:TU|isolate:Control4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C4 C4 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0016_good_1.fq.gz Unknown_BO623-04T0016_good_2.fq.gz fastq fastq 6210972784.0 20767744.0 Unknown BO623 04T0016 good 1.fq.gz 0:149.53 1:149.53 A:1591917700;C:1506245368;G:1529628371;T:1583090947;N:90398 149 149     1591917700 1506245368 1529628371 1583090947 90398 SRX24880737 SRS21589514 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32624 32624 SRR29366301 SRX24880736 SRS21589513 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C3   strain:TU|isolate:Control3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C3 C3 A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0015_good_1.fq.gz Unknown_BO623-04T0015_good_2.fq.gz fastq fastq 6666249022.0 22284306.0 Unknown BO623 04T0015 good 1.fq.gz 0:149.57 1:149.57 A:1722337869;C:1610144787;G:1630507947;T:1703082771;N:175648 149 149     1722337869 1610144787 1630507947 1703082771 175648 SRX24880736 SRS21589513 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32625 32625 SRR29366302 SRX24880735 SRS21589512 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs6   strain:TU|isolate:NPs6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs6 NPs6 A total amount of11 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0024_good_1.fq.gz Unknown_BO623-04T0024_good_2.fq.gz fastq fastq 6819262402.0 22797722.0 Unknown BO623 04T0024 good 1.fq.gz 0:149.56 1:149.56 A:1781861689;C:1629655448;G:1645382478;T:1762184452;N:178335 149 149     1781861689 1629655448 1645382478 1762184452 178335 SRX24880735 SRS21589512 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32626 32626 SRR29366303 SRX24880734 SRS21589511 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs5   strain:TU|isolate:NPs5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs5 NPs5 A total amount of10 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0023_good_1.fq.gz Unknown_BO623-04T0023_good_2.fq.gz fastq fastq 6773730348.0 22673915.0 Unknown BO623 04T0023 good 1.fq.gz 0:149.37 1:149.37 A:1779182337;C:1607164031;G:1624141377;T:1763062617;N:179986 149 149     1779182337 1607164031 1624141377 1763062617 179986 SRX24880734 SRS21589511 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32627 32627 SRR29366304 SRX24880733 SRS21589509 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C2   strain:TU|isolate:Control2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C2 C2 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following manufacturers recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37C for 15 min followed by 5 min at 95C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0014_good_1.fq.gz Unknown_BO623-04T0014_good_2.fq.gz fastq fastq 6805354296.0 22755187.0 Unknown BO623 04T0014 good 1.fq.gz 0:149.53 1:149.53 A:1742825793;C:1651738009;G:1677448209;T:1733168084;N:174201 149 149     1742825793 1651738009 1677448209 1733168084 174201 SRX24880733 SRS21589509 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32628 32628 SRR29366305 SRX24880732 SRS21589510 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C1   strain:TU|isolate:Control1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C1 C1 A total amount of 0 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0013_good_1.fq.gz Unknown_BO623-04T0013_good_2.fq.gz fastq fastq 6546144006.0 21896126.0 Unknown BO623 04T0013 good 1.fq.gz 0:149.48 1:149.48 A:1688579059;C:1582023304;G:1598552166;T:1676633897;N:355580 149 149     1688579059 1582023304 1598552166 1676633897 355580 SRX24880732 SRS21589510 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
36695 36695 SRR831692 SRX269410 SRS415075 SRP021210 PRJNA197389 Danio rerio strain:Wildtype strains AB WIK and AB/Tueb Transcriptome or Gene expression PRJNA197389 Transcriptome Analysis Gene expression profiling of several wildtype strains of zebrafish embryos. The samples were pooled from several developmental stages ranging from 2 dpf to 7 dpf This breadth of sampling gives a broad idea of genes expressed during early development and SNPs associated with wildtype strains.   pubmed:23299976   RNA seq from Fred Hutchinscon AB strain of Danio rerio AB FH.bam   geo loc name:USA: Seattle WA|isolation source:zebrafish embryos|subspecf gen lin:AB from Fred Hutchinson|dev stage:mix of 2 dpf 7 dpf type:pool of multiple embryos from each develomental stage|strain:AB                 AB FH AB FH 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP021210     FH_AB.bam bam 2246623442.0 24070720.0 AB FH 0:49 1:49 A:574600075;C:551290408;G:541354340;T:579331239;N:47380 49 49     574600075 551290408 541354340 579331239 47380 SRX269410 SRS415075 SRA073810 Fred Hutchinson Cancer Research Center|Moens Fred Hutchinson Cancer Research Center 2 0.96858 0.96855 0.08369 0.08397 0.67953 0.67959 0.45983 0.44926 49 49 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   United States 2014-04-19 Multi-stage Multi-stage Whole Organism All anatomical structures
42451 42451 SRR5590336 SRX2847138 SRS2220119 SRP115073 PRJNA387549 zebrafish Raw sequence reads PRJNA387549 Metagenomics The study was to unravel the complex toxic effects of chemical contaminants on the health of organisms as based on different levels of biological profling.       without xxx and with difenoconazole CK D 50 D 500   strain:AB|isolate:embryo|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:pooled male and female|tissue:whole individual|BioSampleModel:Model organism or animal                 RNA Sequencing in zebrafish without xxx and with difenoconazole zebrafish RNA Sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>6</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP115073     CK_1_1.fq.gz CK_1_2.fq.gz CK_2_1.fq.gz CK_3_1.fq.gz CK_3_2.fq.gz D_500_1_1.fq.gz D_500_1_2.fq.gz D_500_2_1.fq.gz D_500_2_2.fq.gz D_500_3_1.fq.gz D_500_3_2.fq.gz D_50_1_1.fq.gz D_50_1_2.fq.gz D_50_3_2.fq.gz D_50_3_1.fq.gz D_50_2_2.fq.gz D_50_2_1.fq.gz CK_2_2.fq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 81797448900.0 272658163.0 zebrafish RNA Seq 0:150 1:150 A:21743331485;C:19042575463;G:19378823851;T:21630253992;N:2464109 150 150     21743331485 19042575463 19378823851 21630253992 2464109 SRX2847138 SRS2220119 SRA564978 China Agricultural University|College of Science China Agricultural University 2 0.91941 0.92018 0.10515 0.10533 0.67939 0.68552 0.46739 0.46494 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2020-04-14 Undetermined 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
58872 58872 SRR11510448 SRX8082500 SRS6450585 SRP255712 PRJNA623798 Single cell lineage tracing on endogenous scarring sites scLOESS PRJNA623798 Other Lineage recording of zebrafish embryogenesis reveals early cell fate commitment     The developmental history of a whole zebrafish organism were recording by LOESS Lineage tracing Of Endogenous Scarring Sites technique. And both cell lineage histories and cell molecular profile were reconstructed by single cell RNA Seq profiling with the help of single cell sequencing methods and self developed analysis strategies. Single Cell RNA Seq of a whole organism of zebrafish larva SC   strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal                 Single Cell RNA Seq of a whole organism of zebrafish larva SC L3 SC L3 Zebrafish embryo at one cell stage were micro injected with gRNA pool and Cas9 mRNA mixture and growth at standard condiction ttwo xxxdpf. Then a single larva were lysis into single cell suspension and the RNA profile were obtained by 10x Genomics Chromium Single Cell three prime Reagent Kits v2 Chemistry.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP255712     SC-I1_S1_L001_R1_001.fastq.gz SC-I1_S1_L001_R2_001.fastq.gz SC-I1_S1_L002_R1_001.fastq.gz SC-I1_S1_L002_R2_001.fastq.gz SC-I1_S1_L003_R1_001.fastq.gz SC-I1_S1_L003_R2_001.fastq.gz SC-I2_S1_L001_R1_001.fastq.gz SC-I2_S1_L001_R2_001.fastq.gz SC-I2_S1_L002_R1_001.fastq.gz SC-I2_S1_L002_R2_001.fastq.gz SC-I2_S1_L003_R1_001.fastq.gz SC-I2_S1_L003_R2_001.fastq.gz SC-I3_S1_L001_R1_001.fastq.gz SC-I3_S1_L001_R2_001.fastq.gz SC-I3_S1_L002_R1_001.fastq.gz SC-I3_S1_L002_R2_001.fastq.gz SC-I3_S1_L003_R1_001.fastq.gz SC-I3_S1_L003_R2_001.fastq.gz SC-I4_S1_L001_R1_001.fastq.gz SC-I4_S1_L001_R2_001.fastq.gz SC-I4_S1_L002_R1_001.fastq.gz SC-I4_S1_L002_R2_001.fastq.gz SC-I4_S1_L003_R1_001.fastq.gz SC-I4_S1_L003_R2_001.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 86925323584.0 493893884.0 SC I1 S1 L001 R1 001.fastq.gz 0:26 1:150 A:24075189135;C:19816237204;G:21200277502;T:21828035227;N:5584516 26 150     24075189135 19816237204 21200277502 21828035227 5584516 SRX8082500 SRS6450585 SRA1063827 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.00528 0.77254 0.00115 0.06529 0.98729 0.8158 0.41854 0.50141 26 150 T B sc-like readlen illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   China 2020-04-11 Larval Larval Whole Organism All anatomical structures
67034 67034 SRR16991903 SRX13182261 SRS11111533 SRP347063 PRJNA782235 Nano Palladium free transcriptomic analysis in a non human model organism Danio rerio PRJNA782235 Other The effects of free nano palladium in zebrafish Danio rerio was determined using transcriptome sequencing. The purity of mRNA from the control fishes were checked and the processed reads were mapped with the reference genome of Danio rerio. Around 67835 genes were expressed in control with respect to the total reads. The expressed genes showed no changes in their behaviour which is evident that the fishes without xxx exposure of xenobiotics caused no changes.         BUANControl   strain:AB strain Wild type|age:6 month|dev stage:adult|sex:male|tissue:Whole fish tissue|collection date:2021 03 06|store cond:Liquid Nitrogen|treatment:Nil|BioSampleModel:Model organism or animal                 NP free study on Zebrafish C1 Control NPfree Zebrafish C1 Control NPfree Zebrafish Palladium nanoparticles Pd NPs have been the reliable substitutes as conventional catalysts for its high efficiency and conversion of CO hydrocarbons and NO into less harmful CO2 water and nitrogen. Due to surface abrasion of converters Pd as ultrafine/nanoparticles are liberated into the environment causing possible health effects. Also Pd might reach the aquatic system through heavy precipitation and runoff. Here we aimed to profile the transcriptome of Danio rerio exposed to nano palladium at environmentally relevant concentrations with control. 500 ng of total RNA of nano Pd free fishes Control was isolated and the enriched mRNAs were reverse transcribed to form cDNA. The purified amplified cDNA library was eluted in the TE buffer. The concentrations above 2 ng/µL were used for the transcriptome analysis with the reference genome. In the control group 67835 genes were expressed which showed no changes in their behavior.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 1000   SRP347063     Control_R1.fastq Control_R2.fastq fastq fastq 4526842200.0 15089474.0 Control R1.fastq 0:150 1:150 A:1257431594;C:1009220672;G:1028452096;T:1231606739;N:131099 150 150     1257431594 1009220672 1028452096 1231606739 131099 SRX13182261 SRS11111533 SRA1332407 Bharathiar University|Zoology Bharathiar University 2 0.84019 0.84256 0.12963 0.12905 0.70266 0.70761 0.54173 0.54265 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   India 2021-11-21 Adult Adult Whole Organism All anatomical structures
67036 67036 SRR17001172 SRX13191392 SRS11119484 SRP347216 PRJNA782554 Transcriptome profiling of environmental relevant low concentrations 0.4 ng/L of nano Palladium in Danio rerio PRJNA782554 Other The effects of nano palladium 0.4 ng per L in zebrafish Danio rerio was determined using transcriptome sequencing. The purity of mRNA from the control and nano Pd exposed fishes were checked and the processed reads were mapped with the reference genome of Danio rerio. Around 64792 genes were expressed in Treatment II respectively with respect to the total reads. There were 3153 differentially expressed genes in Control vs Treatment II with 2900 up regulated and 253 down regulated genes. Also for Treatment I vs Treatment II 3347 genes were significantly differentially expressed with 2101 up regulated and 1246 down regulated genes. The up regulation and down regulation of the genes were evident that the nano Pd can affect the physiological and endocrine functions of zebrafish.         BUANNPd0.4ng   strain:AB strain Wild Type|age:6 mpf|dev stage:Adult|sex:male|tissue:Whole Fish Tissue|collection date:2021 03 06|store cond:Liquid Nitrogen|treatment:0.4 ng/L nano Palladium|BioSampleModel:Model organism or animal                 0.4 ng/L nano Pd exposed Zebrafish nano Pd0.4ng nano Pd0.4ng Palladium nanoparticles Pd NPs have been the reliable substitutes as conventional catalysts for its high efficiency and conversion of CO hydrocarbons and NO into less harmful CO2 water and nitrogen. Due to surface abrasion of converters Pd as ultrafine/nanoparticles are liberated into the environment causing possible health effects. Also Pd leaches to the aquatic system through heavy precipitation and runoff. Here we aimed to profile the transcriptome of Danio rerio exposed to nano palladium at xxx.4 ng/L environmental concentration. 500 ng of total RNA of 0.4 ng/L nano Pd fish was isolated and the enriched mRNAs were reverse transcribed to form cDNA. The concentrations above 2 ng/L were used for the transcriptome analysis with the reference genome. Around 64792 genes were expressed in 0.4 ng/L. There were 3153 DEGs in Control vs 0.4 ng/L with 2900 up regulated and 253 down regulated genes. Also for 22 ng/L vs 0.4 ng/L 3347 genes were significantly expressed with 2101 up regulated and 1246 down regulated genes. The transcriptome screening is evident that nano Pd can cause possible effects in organisms even at low concentrations.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 1000   SRP347216     Treated2_R1.fastq Treated2_R2.fastq fastq fastq 4185717300.0 13952391.0 Treated2 R1.fastq 0:150 1:150 A:1131532349;C:966052110;G:976209681;T:1111787487;N:135673 150 150     1131532349 966052110 976209681 1111787487 135673 SRX13191392 SRS11119484 SRA1332836 ANILA P ASHOKAN|BHARATHIAR UNIVERSITY ZOOLOGY DEPARTEMNT ANILA P ASHOKAN 2 0.90097 0.90521 0.05086 0.0512 0.71969 0.72403 0.45845 0.45942 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   Unknown 2021-11-22 Adult Adult Whole Organism All anatomical structures
68542 68542 SRR17994489 SRX14150133 SRS11975603 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         psip1aMO 3   strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos psip1a MO psip1a MO3 psip1a MO3 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 PSIP1AMO_experiment3_sorted.bam bam 8445901500.0 28153005.0 PSIP1AMO experiment3 sorted.bam 0:150 1:150 A:2261122354;C:1981306733;G:1972898831;T:2230317126;N:256456 150 150     2261122354 1981306733 1972898831 2230317126 256456 SRX14150133 SRS11975603 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.94991 0.94968 0.08913 0.0893 0.68525 0.68621 0.46191 0.46633 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
68543 68543 SRR17994490 SRX14150132 SRS11975602 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         psip1aMO 2   strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos psip1a MO psip1a MO2 psip1a MO2 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 PSIP1AMO_experiment2_sorted.bam bam 7506678900.0 25022263.0 PSIP1AMO experiment2 sorted.bam 0:150 1:150 A:1988273906;C:1776222092;G:1777720261;T:1964233379;N:229262 150 150     1988273906 1776222092 1777720261 1964233379 229262 SRX14150132 SRS11975602 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.95224 0.95202 0.07188 0.07212 0.68 0.6789 0.46391 0.46353 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
68544 68544 SRR17994491 SRX14150131 SRS11975601 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         psip1aMO 1   strain:EKW|isolate:embryos injected with psip1a MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos psip1a MO psip1a MO1 psip1a MO1 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 PSIP1AMO_experiment1_sorted.bam bam 6695117700.0 22317059.0 PSIP1AMO experiment1 sorted.bam 0:150 1:150 A:1786397578;C:1577152264;G:1568675842;T:1762687628;N:204388 150 150     1786397578 1577152264 1568675842 1762687628 204388 SRX14150131 SRS11975601 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.95203 0.95199 0.07618 0.07659 0.6845 0.68495 0.46729 0.46789 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
68545 68545 SRR17994492 SRX14150130 SRS11975600 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         mispairedMO 3   strain:EKW|isolate:embryos injected with control MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos control MO control MO3 control MO3 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 mispairedMO_experiment3_sorted.bam bam 7624971600.0 25416572.0 mispairedMO experiment3 sorted.bam 0:150 1:150 A:2025714467;C:1802766527;G:1804286259;T:1991972887;N:231460 150 150     2025714467 1802766527 1804286259 1991972887 231460 SRX14150130 SRS11975600 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.95243 0.95241 0.08077 0.08052 0.69323 0.69422 0.47383 0.47347 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
68546 68546 SRR17994493 SRX14150129 SRS11975599 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         mispairedMO 2   strain:EKW|isolate:embryos injected with control MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos control MO control MO2 control MO2 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 mispairedMO_experiment2_sorted.bam bam 6644627100.0 22148757.0 mispairedMO experiment2 sorted.bam 0:150 1:150 A:1760529385;C:1574258759;G:1574657792;T:1734978260;N:202904 150 150     1760529385 1574258759 1574657792 1734978260 202904 SRX14150129 SRS11975599 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.95205 0.95138 0.07964 0.07993 0.69321 0.69337 0.45954 0.46053 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
68547 68547 SRR17994494 SRX14150128 SRS11975598 SRP359470 PRJNA806206 RNA seq for psip1a knockdown PRJNA806206 Other Transcription coactivators function in a variety of ways which effectively facilitate the process of transcription and play an essential role in gene regulation. Among them Psip1 the gene codes LEDGF/p75 has been implicated in cancer autoimmune diseases and HIV pathogenesis. However the function of psip1 in vascular development is not known. The goal of this study is to reveal the RNA expression profile using zebrafish embryos when decreasing the expression of psip1a.         mispairedMO 1   strain:EKW|isolate:embryos injected with control MO|breed:N/A|cultivar:N/A|ecotype:N/A|age:24 hpf|dev stage:Segmentation|sex:N/A|tissue:whole embryo|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish embryos control MO control MO1 control MO1 The cDNA Library construction and quality control were coordinated by Novogen co. Ltd     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP359470   assembly:GRCz10 mispairedMO_experiment1_sorted.bam bam 5511040500.0 18370135.0 mispairedMO experiment1 sorted.bam 0:150 1:150 A:1464768264;C:1302363618;G:1300763319;T:1442976922;N:168377 150 150     1464768264 1302363618 1300763319 1442976922 168377 SRX14150128 SRS11975598 SRA1370574 UC Merced|Bioengineering UC Merced 2 0.95157 0.95216 0.07714 0.07754 0.68874 0.68905 0.4719 0.47446 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   United States 2022-02-11 Multi-stage Embryo Whole Organism All anatomical structures
71545 71545 SRR21784852 SRX17779292 SRS15305447 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio Normal diet 1 1 CD36 normal diet 1 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 normal diet fish 1 1 C15D 12 1 1 C15D 12 1 1 the zebrafish larvae fed with normal diet from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     C15D_12_1_1_paired C15D_12_1_2_paired fastq fastq 5223003761.0 17590299.0 C15D 12 1 1 paired 0:148.55 1:148.38 A:1369931254;C:1227975299;G:1223263204;T:1401778621;N:55383 148 148     1369931254 1227975299 1223263204 1401778621 55383 SRX17779292 SRS15305447 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.94554 0.94659 0.11224 0.11161 0.71898 0.71849 0.56127 0.55388 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71546 71546 SRR21784853 SRX17779291 SRS15305446 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio CACF 2 1 CD36 CACF 2 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 with CACF treatment fish 1 1 T15D 24 C 2 1 T15D 24 C 2 1 the zebrafish larvae fed with hight fat diet and treat with CACF everyday from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     T15D_24_C_2_1_paired T15D_24_C_2_2_paired fastq fastq 3981831028.0 13417594.0 T15D 24 C 2 1 paired 0:148.59 1:148.17 A:1093541197;C:886197071;G:886629442;T:1115421463;N:41855 148 148     1093541197 886197071 886629442 1115421463 41855 SRX17779291 SRS15305446 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.94081 0.94152 0.10901 0.10793 0.70964 0.70855 0.602 0.60183 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71547 71547 SRR21784854 SRX17779290 SRS15305445 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio CACF 4 1 CD36 CACF 4 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 with CACF treatment fish 2 1 T15D 24 C 4 1 T15D 24 C 4 1 the zebrafish larvae fed with hight fat diet and treat with CACF everyday from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     T15D_24_C_4_1_paired T15D_24_C_4_2_paired fastq fastq 4676812747.0 15766218.0 T15D 24 C 4 1 paired 0:148.04 1:148.60 A:1264847140;C:1061075206;G:1060248997;T:1290593882;N:47522 148 148     1264847140 1061075206 1060248997 1290593882 47522 SRX17779290 SRS15305445 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.92949 0.93109 0.12219 0.12166 0.70343 0.70122 0.56431 0.56468 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71548 71548 SRR21784855 SRX17779289 SRS15305444 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio Normal diet 2 1 CD36 normal diet 2 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 normal diet fish 2 1 C15D 12 2 1 C15D 12 2 1 the zebrafish larvae fed with normal diet from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     C15D_12_2_1_paired C15D_12_2_2_paired fastq fastq 4709835299.0 15889935.0 C15D 12 2 1 paired 0:148.38 1:148.02 A:1276830997;C:1066019825;G:1064609195;T:1302325802;N:49480 148 148     1276830997 1066019825 1064609195 1302325802 49480 SRX17779289 SRS15305444 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.92935 0.9298 0.13602 0.1343 0.70747 0.70788 0.50602 0.50503 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval 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");;