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run_metadata

26 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RANDOM" and tissue_curation = "Eye"

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devstage_curation_coarse 3

devstage_curation 3

tissue_curation_coarse 1

tissue_curation 1

  • Eye · 26 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 26 ✖

experiment.library_layout 1

  • PAIRED · 26 ✖
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
57197 57197 SRR11267492 SRX7874162 SRS6282467 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME wt 3   strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 wild type male eyes replicate 3 ME wt 3 ME wt 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-23-W3ME_RRA121665-V_2.fq.gz s-23-W3ME_RRA121665-V_1.fq.gz fastq fastq 8400228000.0 28000760.0 s 23 W3ME RRA121665 V 1.fq.gz 0:150 1:150 A:2303053910;C:1920194253;G:1910340116;T:2266331748;N:307973 150 150     2303053910 1920194253 1910340116 2266331748 307973 SRX7874162 SRS6282467 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.93001 0.92886 0.11082 0.10982 0.68866 0.68822 0.48763 0.4906 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57198 57198 SRR11267493 SRX7874161 SRS6282466 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME wt 2   strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 wild type male eyes replicate 2 ME wt 2 ME wt 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-19-W2ME_RRA121661-V_1.fq.gz s-19-W2ME_RRA121661-V_2.fq.gz fastq fastq 6889800000.0 22966000.0 s 19 W2ME RRA121661 V 1.fq.gz 0:150 1:150 A:1880210832;C:1583780885;G:1578593218;T:1846963840;N:251225 150 150     1880210832 1583780885 1578593218 1846963840 251225 SRX7874161 SRS6282466 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9279 0.92649 0.10311 0.10204 0.68532 0.68647 0.48037 0.48511 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57199 57199 SRR11267494 SRX7874160 SRS6282464 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME wt 1   strain:Abtu|ecotype:wild type|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 wild type male eyes replicate 1 ME wt 1 ME wt 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-15-W1ME_RRA121657-V_2.fq.gz s-15-W1ME_RRA121657-V_1.fq.gz fastq fastq 6969091200.0 23230304.0 s 15 W1ME RRA121657 V 1.fq.gz 0:150 1:150 A:1921340190;C:1585088835;G:1576239642;T:1886167585;N:254948 150 150     1921340190 1585088835 1576239642 1886167585 254948 SRX7874160 SRS6282464 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92763 0.92509 0.11658 0.11517 0.68432 0.68653 0.4946 0.49155 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57200 57200 SRR11267495 SRX7874159 SRS6282465 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME mut 3   strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 mutant male eyes replicate 3 ME mut 3 ME mut 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-11-MU3ME_RRA121653-V_1.fq.gz s-11-MU3ME_RRA121653-V_2.fq.gz fastq fastq 6875632800.0 22918776.0 s 11 MU3ME RRA121653 V 1.fq.gz 0:150 1:150 A:1901087754;C:1556469824;G:1548197705;T:1869624741;N:252776 150 150     1901087754 1556469824 1548197705 1869624741 252776 SRX7874159 SRS6282465 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92604 0.92413 0.11832 0.11725 0.67748 0.67949 0.49008 0.49228 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57201 57201 SRR11267496 SRX7874158 SRS6282463 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME mut 2   strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 mutant male eyes replicate 2 ME mut 2 ME mut 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-7-MU2ME_RRA121649-V_1.fq.gz s-7-MU2ME_RRA121649-V_2.fq.gz fastq fastq 6847404900.0 22824683.0 s 7 MU2ME RRA121649 V 1.fq.gz 0:150 1:150 A:1892928093;C:1547660086;G:1542947611;T:1863669155;N:199955 150 150     1892928093 1547660086 1542947611 1863669155 199955 SRX7874158 SRS6282463 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9251 0.92453 0.12038 0.11934 0.68363 0.68381 0.49355 0.49262 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57202 57202 SRR11267497 SRX7874157 SRS6282462 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           ME mut 1   strain:Abtu|ecotype:mutant|dev stage:adult|sex:male|tissue:eye|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 mutant male eyes replicate 1 ME mut 1 ME mut 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-3-MU1ME_RRA121645-V_1.fq.gz s-3-MU1ME_RRA121645-V_2.fq.gz fastq fastq 6878336700.0 22927789.0 s 3 MU1ME RRA121645 V 1.fq.gz 0:150 1:150 A:1905585865;C:1552515358;G:1547182571;T:1872802386;N:250520 150 150     1905585865 1552515358 1547182571 1872802386 250520 SRX7874157 SRS6282462 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92648 0.92449 0.12124 0.11959 0.68688 0.68996 0.48933 0.48791 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57210 57210 SRR11267505 SRX7874149 SRS6282454 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE wt 3   strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 wild type female eyes replicate 3 FE wt 3 FE wt 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-21-W3FE_RRA121663-V_2.fq.gz s-21-W3FE_RRA121663-V_1.fq.gz fastq fastq 7633204500.0 25444015.0 s 21 W3FE RRA121663 V 1.fq.gz 0:150 1:150 A:2091516097;C:1748144881;G:1739108541;T:2054153967;N:281014 150 150     2091516097 1748144881 1739108541 2054153967 281014 SRX7874149 SRS6282454 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9346 0.93156 0.11275 0.11113 0.69027 0.69436 0.47761 0.47697 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57211 57211 SRR11267506 SRX7874148 SRS6282453 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE wt 2   strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 wild type female eyes replicate 2 FE wt 2 FE wt 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-17-W2FE_RRA121659-V_1.fq.gz s-17-W2FE_RRA121659-V_2.fq.gz fastq fastq 6558727800.0 21862426.0 s 17 W2FE RRA121659 V 1.fq.gz 0:150 1:150 A:1802562905;C:1497351051;G:1488752362;T:1769827486;N:233996 150 150     1802562905 1497351051 1488752362 1769827486 233996 SRX7874148 SRS6282453 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92878 0.92365 0.11321 0.11111 0.68517 0.68872 0.49201 0.48744 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57212 57212 SRR11267507 SRX7874147 SRS6282451 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE wt 1   strain:Abtu|ecotype:wild type|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 wild type female eyes replicate 1 FE wt 1 FE wt 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-13-W1FE_RRA121655-V_1.fq.gz s-13-W1FE_RRA121655-V_2.fq.gz fastq fastq 8123083800.0 27076946.0 s 13 W1FE RRA121655 V 1.fq.gz 0:150 1:150 A:2228184139;C:1856303514;G:1847105654;T:2191192871;N:297622 150 150     2228184139 1856303514 1847105654 2191192871 297622 SRX7874147 SRS6282451 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92966 0.92938 0.1125 0.11144 0.68678 0.68777 0.48758 0.48653 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57213 57213 SRR11267508 SRX7874146 SRS6282450 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE mut 3   strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 mutant female eyes replicate 3 FE mut 3 FE mut 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-9-MU3FE_RRA121651-V_1.fq.gz s-9-MU3FE_RRA121651-V_2.fq.gz fastq fastq 6656295300.0 22187651.0 s 9 MU3FE RRA121651 V 1.fq.gz 0:150 1:150 A:1847801770;C:1499187682;G:1491392362;T:1817671236;N:242250 150 150     1847801770 1499187682 1491392362 1817671236 242250 SRX7874146 SRS6282450 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92627 0.92542 0.122 0.12099 0.68067 0.68166 0.48197 0.48852 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57214 57214 SRR11267509 SRX7874145 SRS6282449 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE mut 2   strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 mutant female eyes replicate 2 FE mut 2 FE mut 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-5-MU2FE_RRA121647-V_1.fq.gz s-5-MU2FE_RRA121647-V_2.fq.gz fastq fastq 7413634500.0 24712115.0 s 5 MU2FE RRA121647 V 1.fq.gz 0:150 1:150 A:2065563537;C:1663387773;G:1656105625;T:2028307360;N:270205 150 150     2065563537 1663387773 1656105625 2028307360 270205 SRX7874145 SRS6282449 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92762 0.92397 0.12723 0.12529 0.68984 0.694 0.49347 0.47963 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
57215 57215 SRR11267510 SRX7874144 SRS6282452 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           FE mut 1   strain:Abtu|ecotype:mutant|dev stage:adult|sex:female|tissue:eye|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 mutant female eyes replicate 1 FE mut 1 FE mut 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-1-MU1FE_RRA121643-V_1.fq.gz s-1-MU1FE_RRA121643-V_2.fq.gz fastq fastq 6864021300.0 22880071.0 s 1 MU1FE RRA121643 V 1.fq.gz 0:150 1:150 A:1901112450;C:1549381718;G:1544210321;T:1869066007;N:250804 150 150     1901112450 1549381718 1544210321 1869066007 250804 SRX7874144 SRS6282452 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.92425 0.92283 0.12022 0.1186 0.68613 0.68716 0.48698 0.49353 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Adult Adult Eye Sensory System
67527 67527 SRR17221754 SRX13401340 SRS11304399 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         cep290 retina 4   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:cep290|Biological replicates:4|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish cep290 mutant retina GC SG 620 8 GC SG 620 8 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_8_S8_L001_R1_001.fastq.gz GC.SG.620_8_S8_L001_R2_001.fastq.gz fastq fastq 38697433494.0 128137197.0 GC.SG.620 8 S8 L001 R1 001.fastq.gz 0:151 1:151 A:10897381553;C:8539501524;G:8224720333;T:11035084087;N:745997 151 151     10897381553 8539501524 8224720333 11035084087 745997 SRX13401340 SRS11304399 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.66646 0.66004 0.33083 0.32152 0.77684 0.77871 0.51619 0.52281 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67528 67528 SRR17221755 SRX13401339 SRS11304398 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         cep290 retina 3   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:cep290|Biological replicates:3|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish cep290 mutant retina GC SG 620 7 GC SG 620 7 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_7_S7_L001_R1_001.fastq.gz GC.SG.620_7_S7_L001_R2_001.fastq.gz fastq fastq 40407223708.0 133798754.0 GC.SG.620 7 S7 L001 R1 001.fastq.gz 0:151 1:151 A:11339805352;C:9005002277;G:8600624695;T:11460947185;N:844199 151 151     11339805352 9005002277 8600624695 11460947185 844199 SRX13401339 SRS11304398 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.65733 0.65156 0.33459 0.32709 0.77952 0.78007 0.53039 0.51873 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67529 67529 SRR17221756 SRX13401338 SRS11304397 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         cep290 retina 2   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:cep290|Biological replicates:2|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish cep290 mutant retina GC SG 620 6 GC SG 620 6 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_6_S6_L001_R1_001.fastq.gz GC.SG.620_6_S6_L001_R2_001.fastq.gz fastq fastq 35177430214.0 116481557.0 GC.SG.620 6 S6 L001 R1 001.fastq.gz 0:151 1:151 A:9864372223;C:7781916441;G:7479621981;T:10050875158;N:644411 151 151     9864372223 7781916441 7479621981 10050875158 644411 SRX13401338 SRS11304397 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.66029 0.65697 0.32728 0.32142 0.7783 0.77522 0.53642 0.5381 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67530 67530 SRR17221757 SRX13401337 SRS11304396 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         cep290 retina 1   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:cep290|Biological replicates:1|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish cep290 mutant retina GC SG 620 5 GC SG 620 5 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_5_S5_L001_R1_001.fastq.gz GC.SG.620_5_S5_L001_R2_001.fastq.gz fastq fastq 38272092466.0 126728783.0 GC.SG.620 5 S5 L001 R1 001.fastq.gz 0:151 1:151 A:10830892004;C:8426926025;G:8067309850;T:10946162775;N:801812 151 151     10830892004 8426926025 8067309850 10946162775 801812 SRX13401337 SRS11304396 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.65684 0.64515 0.33008 0.31832 0.78031 0.78194 0.53178 0.53091 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67531 67531 SRR17221758 SRX13401336 SRS11304395 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         wild type retina 4   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:wild type|Biological replicates:4|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish wild type retina GC SG 620 4 GC SG 620 4 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_4_S4_L001_R1_001.fastq.gz GC.SG.620_4_S4_L001_R2_001.fastq.gz fastq fastq 32602935480.0 107956740.0 GC.SG.620 4 S4 L001 R1 001.fastq.gz 0:151 1:151 A:9278245354;C:7208634191;G:6856278967;T:9259105244;N:671724 151 151     9278245354 7208634191 6856278967 9259105244 671724 SRX13401336 SRS11304395 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.6468 0.64033 0.32923 0.32003 0.77977 0.78299 0.50698 0.5109 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67532 67532 SRR17221759 SRX13401335 SRS11304394 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         wild type retina 3   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:wild type|Biological replicates:3|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish wild type retina GC SG 620 3 GC SG 620 3 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_3_S3_L001_R1_001.fastq.gz GC.SG.620_3_S3_L001_R2_001.fastq.gz fastq fastq 33920268842.0 112318771.0 GC.SG.620 3 S3 L001 R1 001.fastq.gz 0:151 1:151 A:9639086006;C:7411263175;G:7053516817;T:9815703633;N:699211 151 151     9639086006 7411263175 7053516817 9815703633 699211 SRX13401335 SRS11304394 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.65174 0.64442 0.33877 0.32993 0.77875 0.78123 0.51364 0.52557 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67533 67533 SRR17221760 SRX13401334 SRS11304393 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         wild type retina 2   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:wild type|Biological replicates:2|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish wild type retina GC SG 620 2 GC SG 620 2 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_2_S2_L001_R1_001.fastq.gz GC.SG.620_2_S2_L001_R2_001.fastq.gz fastq fastq 30605822768.0 101343784.0 GC.SG.620 2 S2 L001 R1 001.fastq.gz 0:151 1:151 A:8456172381;C:6948566987;G:6670164511;T:8530293907;N:624982 151 151     8456172381 6948566987 6670164511 8530293907 624982 SRX13401334 SRS11304393 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.62585 0.61421 0.29606 0.28346 0.78508 0.78683 0.53231 0.5408 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
67534 67534 SRR17221761 SRX13401333 SRS11304392 SRP350597 PRJNA787536 Danio rerio Raw sequence reads PRJNA787536 Other RNA seq data from adult retina tissue obtained from wild type and cep290 mutant zebrafish at 6 mpf.         wild type retina 1   strain:AB/Ekwill hybrid|isolate:Single individual retina|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 mpf stage:Adult|sex:unknown|tissue:Retina|birth date:2020 09 02|collected by:Sarah Grabinski|collection date:2021 04 24|genotype:wild type|Biological replicates:1|BioSampleModel:Model organism or animal                 RNA seq of 6 mpf adult zebrafish wild type retina GC SG 620 1 GC SG 620 1 RNA isolated from single retina prepared using Illumina stranded mRNA kits     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   SRP350597     GC.SG.620_1_S1_L001_R1_001.fastq.gz GC.SG.620_1_S1_L001_R2_001.fastq.gz fastq fastq 31969773756.0 105860178.0 GC.SG.620 1 S1 L001 R1 001.fastq.gz 0:151 1:151 A:8889341732;C:7177178690;G:6928940526;T:8973631071;N:681737 151 151     8889341732 7177178690 6928940526 8973631071 681737 SRX13401333 SRS11304392 SRA1342775 Cleveland Clinic|Ophthalmic Research Cleveland Clinic 2 0.67113 0.66355 0.32731 0.31578 0.78399 0.78593 0.53938 0.5511 151 151 B B biological fallback assumption illumina novaseq_era unknown random_priming trueseq bulk unknown unknown   United States 2021-12-13 Adult Adult Eye Sensory System
69473 69473 SRR18712322 SRX14812929 SRS12569572 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 72hpf WT b   strain:WT|dev stage:72 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 72 hpf larvae WT for the eMIC domain of srrm3. Eye 72hpf WT Eye 72hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_72hpf_WT_b_R1-125.fq.gz Eye_72hpf_WT_b_R2-125.fq.gz fastq fastq 13437032500.0 53748130.0 Eye 72hpf WT b R1 125.fq.gz 0:125 1:125 A:3455929483;C:3259662773;G:3290102413;T:3423551193;N:7786638 125 125     3455929483 3259662773 3290102413 3423551193 7786638 SRX14812929 SRS12569572 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97078 0.97143 0.04457 0.04373 0.68312 0.68594 0.4516 0.45911 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Larval Larval Eye Sensory System
69474 69474 SRR18712323 SRX14812928 SRS12569571 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 72hpf MUT b   strain:srrm3 MUT|dev stage:72 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 72 hpf larvae mutated for the eMIC domain of srrm3. Eye 72hpf MUT Eye 72hpf MUT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_72hpf_MUT_b_R1-125.fq.gz Eye_72hpf_MUT_b_R2-125.fq.gz fastq fastq 14446388500.0 57785554.0 Eye 72hpf MUT b R1 125.fq.gz 0:125 1:125 A:3747033220;C:3473175271;G:3502836837;T:3715008771;N:8334401 125 125     3747033220 3473175271 3502836837 3715008771 8334401 SRX14812928 SRS12569571 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.96991 0.97029 0.04938 0.04899 0.6813 0.68613 0.44741 0.44599 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Larval Larval Eye Sensory System
69475 69475 SRR18712324 SRX14812927 SRS12569570 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 60hpf WT b   strain:WT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 60 hpf larvae WT for the eMIC domain of srrm3. Eye 60hpf WT Eye 60hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_60hpf_WT_b_R1-125.fq.gz Eye_60hpf_WT_b_R2-125.fq.gz fastq fastq 15250592500.0 61002370.0 Eye 60hpf WT b R1 125.fq.gz 0:125 1:125 A:3923837289;C:3702942025;G:3742033933;T:3872922356;N:8856897 125 125     3923837289 3702942025 3742033933 3872922356 8856897 SRX14812927 SRS12569570 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97168 0.9731 0.0527 0.05258 0.69891 0.70041 0.45973 0.45381 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69476 69476 SRR18712325 SRX14812926 SRS12569569 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 60hpf MUT b   strain:srrm3 MUT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 60 hpf larvae mutated for the eMIC domain of srrm3. Eye 60hpf MUT Eye 60hpf MUT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_60hpf_MUT_b_R1-125.fq.gz Eye_60hpf_MUT_b_R2-125.fq.gz fastq fastq 14932544250.0 59730177.0 Eye 60hpf MUT b R1 125.fq.gz 0:125 1:125 A:3891825609;C:3575114135;G:3598083383;T:3858808039;N:8713084 125 125     3891825609 3575114135 3598083383 3858808039 8713084 SRX14812926 SRS12569569 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.96985 0.97098 0.06006 0.0593 0.68939 0.6926 0.46001 0.45867 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69477 69477 SRR18712326 SRX14812925 SRS12569568 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 48hpf WT b   strain:WT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 48 hpf larvae WT for the eMIC domain of srrm3. Eye 48hpf WT Eye 48hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_48hpf_WT_b_R1-125.fq.gz Eye_48hpf_WT_b_R2-125.fq.gz fastq fastq 15736041750.0 62944167.0 Eye 48hpf WT b R1 125.fq.gz 0:125 1:125 A:4076543478;C:3787178416;G:3834447099;T:4028745594;N:9127163 125 125     4076543478 3787178416 3834447099 4028745594 9127163 SRX14812925 SRS12569568 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97095 0.97209 0.05101 0.05067 0.69408 0.69767 0.47501 0.47714 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69478 69478 SRR18712327 SRX14812924 SRS12569567 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 48hpf MUT b   strain:srrm3 MUT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 48 hpf larvae mutated for the eMIC domain of srrm3. Eye 48hpf MUT Eye 48hpf MUT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_48hpf_MUT_b_R1-125.fq.gz Eye_48hpf_MUT_b_R2-125.fq.gz fastq fastq 14845531750.0 59382127.0 Eye 48hpf MUT b R1 125.fq.gz 0:125 1:125 A:3879709745;C:3539390575;G:3573173326;T:3844623832;N:8634272 125 125     3879709745 3539390575 3573173326 3844623832 8634272 SRX14812924 SRS12569567 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.9684 0.97006 0.05578 0.05498 0.69183 0.69581 0.472 0.46674 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System

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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");;