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run_metadata

32 rows where experiment.library_selection = "PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Undetermined"

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devstage_curation_coarse 4

experiment.library_strategy 3

devstage_curation 3

experiment.library_layout 2

tissue_curation_coarse 1

  • Undetermined · 32 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 32 ✖

experiment.library_selection 1

  • PCR · 32 ✖
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
30250 30250 SRR27756860 SRX23421865 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample A 1 1 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a1.R2.fq.gz cobll1a1.R1.fq.gz fastq fastq 7119566009.0 24893517.0 cobll1a1.R1.fq.gz 0:143.02 1:142.98 A:1899718926;C:1652762152;G:1669973661;T:1897092278;N:18992 143 142     1899718926 1652762152 1669973661 1897092278 18992 SRX23421865 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95825 0.95956 0.0788 0.07795 0.67894 0.67884 0.48342 0.48268 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30251 30251 SRR27756861 SRX23421864 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample L 11 11 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu3.R1.fq.gz tu3.R2.fq.gz fastq fastq 6881670461.0 24208326.0 tu3.R1.fq.gz 0:142.15 1:142.12 A:1820714788;C:1612866668;G:1629078247;T:1818992861;N:17897 142 142     1820714788 1612866668 1629078247 1818992861 17897 SRX23421864 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95713 0.95821 0.07191 0.07071 0.67801 0.67726 0.48591 0.48501 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30252 30252 SRR27756862 SRX23421863 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample C 3 3 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a2.R1.fq.gz cobll1a2.R2.fq.gz fastq fastq 6639076778.0 23213579.0 cobll1a2.R1.fq.gz 0:143.02 1:142.98 A:1799749408;C:1513051586;G:1530064901;T:1796193421;N:17462 143 142     1799749408 1513051586 1530064901 1796193421 17462 SRX23421863 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.95695 0.95781 0.091 0.0896 0.68199 0.68075 0.49051 0.49057 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30253 30253 SRR27756863 SRX23421862 SRS20276790 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       Model organism or animal sample from danio rerio cobll1a   ecotype:missing|dev stage:missing|collection date:2023 02 21|geo loc name:missing|sex:neuter|tissue:FISH|biomaterial provider:missing|z:1000|BioSampleModel:Model organism or animal                 Sample E 5 5 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     cobll1a3.R2.fq.gz cobll1a3.R1.fq.gz fastq fastq 6697695084.0 23490214.0 cobll1a3.R1.fq.gz 0:142.58 1:142.55 A:1755043056;C:1586242926;G:1602146148;T:1754245480;N:17474 142 142     1755043056 1586242926 1602146148 1754245480 17474 SRX23421862 SRS20276790 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96007 0.96224 0.06487 0.06404 0.66939 0.66906 0.48829 0.48765 130 130 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30254 30254 SRR27756864 SRX23421861 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample G 7 7 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu1.R1.fq.gz tu1.R2.fq.gz fastq fastq 7124072376.0 25020568.0 tu1.R1.fq.gz 0:142.38 1:142.35 A:1889928651;C:1664950324;G:1681768417;T:1887406325;N:18659 142 142     1889928651 1664950324 1681768417 1887406325 18659 SRX23421861 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96032 0.96145 0.07398 0.07359 0.68503 0.6843 0.48524 0.48933 116 116 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
30255 30255 SRR27756865 SRX23421860 SRS20276789 SRP486416 PRJNA1069604 Danio rerio strain:TL | breed:Danio rerio Raw sequence reads PRJNA1069604 Other To study the effect of a gene deletion in zebrafish       MIMARKS Specimen sample from Danio rerio WT   strain:WT|collection date:2023 02 28|depth:missing|elev:missing|env broad scale:missing|env local scale:missing|env medium:missing|geo loc name:missing|isol growth condt:missing|lat lon:missing|BioSampleModel:MIMARKS.specimen|BioSampleModel:MIGS/MIMS/MIMARKS.microbial                 Sample J 9 9 common method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP486416     tu2.R1.fq.gz tu2.R2.fq.gz fastq fastq 7024719799.0 24627933.0 tu2.R1.fq.gz 0:142.63 1:142.60 A:1841519314;C:1662861553;G:1679614735;T:1840705226;N:18971 142 142     1841519314 1662861553 1679614735 1840705226 18971 SRX23421860 SRS20276789 SRA1792726 Hunan Normal University|Hunan Normal University Hunan Normal University Hunan Normal University Hunan Normal University 2 0.96006 0.96141 0.06713 0.06631 0.67464 0.67426 0.48684 0.48648 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-01-29 Undetermined Undetermined Undetermined Undetermined
34593 34593 SRR32128857 SRX27475161 SRS23899211 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated4   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable10|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable10|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish10|isolation source:zebrafish10|BioSampleModel:Model organism or animal                 sample info library 10 library 10 DNA barcode10     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated4.read1.fastq.gz lighttreated4.read2.fastq.gz fastq fastq 6388100400.0 21293668.0 lighttreated4.read1.fastq.gz 0:150 1:150 A:1711345062;C:1474552325;G:1531680528;T:1670485285;N:37200 150 150     1711345062 1474552325 1531680528 1670485285 37200 SRX27475161 SRS23899211 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34594 34594 SRR32128858 SRX27475160 SRS23899210 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated3   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable9|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable9|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish9|isolation source:zebrafish9|BioSampleModel:Model organism or animal                 sample info library 9 library 9 DNA barcode9     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated3.read1.fastq.gz lighttreated3.read2.fastq.gz fastq fastq 7919383200.0 26397944.0 lighttreated3.read1.fastq.gz 0:150 1:150 A:2135212601;C:1813586654;G:1892878979;T:2077658764;N:46202 150 150     2135212601 1813586654 1892878979 2077658764 46202 SRX27475160 SRS23899210 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34595 34595 SRR32128859 SRX27475159 SRS23899209 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated2   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable8|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable8|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish8|isolation source:zebrafish8|BioSampleModel:Model organism or animal                 sample info library 8 library 8 DNA barcode8     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated2.read1.fastq.gz lighttreated2.read2.fastq.gz fastq fastq 7060994100.0 23536647.0 lighttreated2.read1.fastq.gz 0:150 1:150 A:1921099545;C:1595276449;G:1668657714;T:1875918159;N:42233 150 150     1921099545 1595276449 1668657714 1875918159 42233 SRX27475159 SRS23899209 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34596 34596 SRR32128860 SRX27475158 SRS23899208 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated1   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable7|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable7|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish7|isolation source:zebrafish7|BioSampleModel:Model organism or animal                 sample info library 7 library 7 DNA barcode7     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated1.read1.fastq.gz lighttreated1.read2.fastq.gz fastq fastq 6908625300.0 23028751.0 lighttreated1.read1.fastq.gz 0:150 1:150 A:1872190225;C:1565342714;G:1644929113;T:1826124355;N:38893 150 150     1872190225 1565342714 1644929113 1826124355 38893 SRX27475158 SRS23899208 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34597 34597 SRR32128861 SRX27475157 SRS23899207 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated6   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable6|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable6|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish6|isolation source:zebrafish6|BioSampleModel:Model organism or animal                 sample info library 6 library 6 DNA barcode6     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated6.read1.fastq.gz darktreated6.read2.fastq.gz fastq fastq 8601630900.0 28672103.0 darktreated6.read1.fastq.gz 0:150 1:150 A:2318530970;C:1973292572;G:2040962638;T:2268796005;N:48715 150 150     2318530970 1973292572 2040962638 2268796005 48715 SRX27475157 SRS23899207 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34598 34598 SRR32128862 SRX27475156 SRS23899206 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated5   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable5|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable5|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish5|isolation source:zebrafish5|BioSampleModel:Model organism or animal                 sample info library 5 library 5 DNA barcode5     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated5.read1.fastq.gz darktreated5.read2.fastq.gz fastq fastq 8265255300.0 27550851.0 darktreated5.read1.fastq.gz 0:150 1:150 A:2224219375;C:1898065838;G:1969603341;T:2173318912;N:47834 150 150     2224219375 1898065838 1969603341 2173318912 47834 SRX27475156 SRS23899206 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34599 34599 SRR32128863 SRX27475155 SRS23899205 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated4   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable4|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable4|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish4|isolation source:zebrafish4|BioSampleModel:Model organism or animal                 sample info library 4 library 4 DNA barcode4     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated4.read1.fastq.gz darktreated4.read2.fastq.gz fastq fastq 8061663600.0 26872212.0 darktreated4.read1.fastq.gz 0:150 1:150 A:2171664867;C:1853256385;G:1909447014;T:2127248788;N:46546 150 150     2171664867 1853256385 1909447014 2127248788 46546 SRX27475155 SRS23899205 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34600 34600 SRR32128864 SRX27475154 SRS23899204 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated3   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable3|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable3|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish3|isolation source:zebrafish3|BioSampleModel:Model organism or animal                 sample info library 3 library 3 DNA barcode3     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated3.read1.fastq.gz darktreated3.read2.fastq.gz fastq fastq 8287650300.0 27625501.0 darktreated3.read1.fastq.gz 0:150 1:150 A:2231337901;C:1902488349;G:1971440974;T:2182335741;N:47335 150 150     2231337901 1902488349 1971440974 2182335741 47335 SRX27475154 SRS23899204 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34601 34601 SRR32128865 SRX27475153 SRS23899203 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated6   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable12|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable12|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish12|isolation source:zebrafish12|BioSampleModel:Model organism or animal                 sample info library 12 library 12 DNA barcode12     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated6.read1.fastq.gz lighttreated6.read2.fastq.gz fastq fastq 7610579400.0 25368598.0 lighttreated6.read1.fastq.gz 0:150 1:150 A:2063115765;C:1733106391;G:1795336188;T:2018975316;N:45740 150 150     2063115765 1733106391 1795336188 2018975316 45740 SRX27475153 SRS23899203 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34602 34602 SRR32128866 SRX27475152 SRS23899202 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         lighttreated5   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable11|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable11|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish11|isolation source:zebrafish11|BioSampleModel:Model organism or animal                 sample info library 11 library 11 DNA barcode11     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     lighttreated5.read1.fastq.gz lighttreated5.read2.fastq.gz fastq fastq 6677234100.0 22257447.0 lighttreated5.read1.fastq.gz 0:150 1:150 A:1812295746;C:1506030273;G:1585674870;T:1773195250;N:37961 150 150     1812295746 1506030273 1585674870 1773195250 37961 SRX27475152 SRS23899202 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34603 34603 SRR32128867 SRX27475151 SRS23899201 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated2   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable2|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable2|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish2|isolation source:zebrafish2|BioSampleModel:Model organism or animal                 sample info library 2 library 2 DNA barcode2     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated2.read1.fastq.gz darktreated2.read2.fastq.gz fastq fastq 8723972700.0 29079909.0 darktreated2.read1.fastq.gz 0:150 1:150 A:2341340036;C:2009282478;G:2082163796;T:2291135873;N:50517 150 150     2341340036 2009282478 2082163796 2291135873 50517 SRX27475151 SRS23899201 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
34604 34604 SRR32128868 SRX27475150 SRS23899200 SRP559934 PRJNA1215774 3 mpf dark reared zebrafish eye RNA sequencing PRJNA1215774 Other Outdoor time and light intensity are important emerging factors affecting myopia; however the underlying mechanisms remain unknown. To clarify the possible molecular mechanisms underlying myopia caused by dark environment 3 mpf zebrafish eye RNA sequencing was performed.         darktreated1   strain:not applicable|isolate:Sun Yat sen University|breed:not applicable1|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable1|collection date:2021 04 16|geo loc name:China: GuangZhou|sex:not applicable|tissue:zebrafish1|isolation source:zebrafish1|BioSampleModel:Model organism or animal                 sample info library 1 library 1 DNA barcode1     WXS TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP559934     darktreated1.read1.fastq.gz darktreated1.read2.fastq.gz fastq fastq 7940928300.0 26469761.0 darktreated1.read1.fastq.gz 0:150 1:150 A:2133717650;C:1824526059;G:1895330033;T:2087310578;N:43980 150 150     2133717650 1824526059 1895330033 2087310578 43980 SRX27475150 SRS23899200 SRA2060897 zhujiang hospital|ophthalmology zhujiang hospital                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-25 Undetermined Adult Undetermined Undetermined
66086 66086 SRR15900240 SRX12190888 SRS10168725 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM+CH 2   strain:AB|isolate:CH2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab CH2 tchenlab CH2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_CH_5.8.IP_R1.fastq.gz EOM_CH_5.8.IP_R2.fastq.gz EOM_CH_5.8.Input_R1.fastq.gz EOM_CH_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 13391108400.0 44637028.0 EOM CH 5.8.IP R1.fastq.gz 0:150 1:150 A:2721241817;C:3886076819;G:4096587749;T:2611313908;N:75888107 150 150     2721241817 3886076819 4096587749 2611313908 75888107 SRX12190888 SRS10168725 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.8442 0.59467 0.17491 0.14724 0.86147 0.89112 0.7593 0.63363 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66087 66087 SRR15900241 SRX12190887 SRS10168724 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM+CH 1   strain:AB|isolate:CH1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab CH1 tchenlab CH1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_CH_4.16.IP_R1.fastq.gz EOM_CH_4.16.IP_R2.fastq.gz EOM_CH_4.16.Input_R1.fastq.gz EOM_CH_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 12428976000.0 41429920.0 EOM CH 4.16.IP R1.fastq.gz 0:150 1:150 A:2486344612;C:3648199763;G:3865825828;T:2365039093;N:63566704 150 150     2486344612 3648199763 3865825828 2365039093 63566704 SRX12190887 SRS10168724 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.91763 0.6223 0.18817 0.15102 0.84891 0.87957 0.74757 0.64429 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66088 66088 SRR15900242 SRX12190886 SRS10168723 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 3   strain:AB|isolate:T3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T3 tchenlab T3 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_5.9.IP_R1.fastq.gz EOM_5.9.IP_R2.fastq.gz EOM_5.9.Input_R1.fastq.gz EOM_5.9.Input_R2.fastq.gz fastq fastq fastq fastq 12301780200.0 41005934.0 EOM 5.9.IP R1.fastq.gz 0:150 1:150 A:2415542475;C:3651603114;G:3847935468;T:2318868176;N:67830967 150 150     2415542475 3651603114 3847935468 2318868176 67830967 SRX12190886 SRS10168723 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.87516 0.65874 0.18282 0.16547 0.85561 0.87657 0.72193 0.61862 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66089 66089 SRR15900243 SRX12190885 SRS10168722 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 2   strain:AB|isolate:T2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T2 tchenlab T2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_5.8.IP_R1.fastq.gz EOM_5.8.IP_R2.fastq.gz EOM_5.8.Input_R1.fastq.gz EOM_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 12373139700.0 41243799.0 EOM 5.8.IP R1.fastq.gz 0:150 1:150 A:2429212483;C:3679585650;G:3865741937;T:2330164654;N:68434976 150 150     2429212483 3679585650 3865741937 2330164654 68434976 SRX12190885 SRS10168722 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.88644 0.67829 0.18408 0.16867 0.84652 0.8704 0.76376 0.64158 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66090 66090 SRR15900244 SRX12190884 SRS10168721 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         EOM 1   strain:AB|isolate:T1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab T1 tchenlab T1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py EOM_4.16.IP_R1.fastq.gz EOM_4.16.IP_R2.fastq.gz EOM_4.16.Input_R1.fastq.gz EOM_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 13638730800.0 45462436.0 EOM 4.16.IP R1.fastq.gz 0:150 1:150 A:2673949221;C:4057121296;G:4266457677;T:2562131972;N:79070634 150 150     2673949221 4057121296 4266457677 2562131972 79070634 SRX12190884 SRS10168721 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.87634 0.65649 0.18403 0.16375 0.85486 0.87913 0.69253 0.6405 150 150 B B mate2-mate1 similar by mapping diff illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66091 66091 SRR15900245 SRX12190883 SRS10168720 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 3   strain:AB|isolate:C3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C3 tchenlab C3 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_5.9.IP_R1.fastq.gz DMSO_5.9.IP_R2.fastq.gz DMSO_5.9.Input_R1.fastq.gz DMSO_5.9.Input_R2.fastq.gz fastq fastq fastq fastq 12477964200.0 41593214.0 DMSO 5.9.IP R1.fastq.gz 0:150 1:150 A:2462053397;C:3697418372;G:3878832850;T:2368512335;N:71147246 150 150     2462053397 3697418372 3878832850 2368512335 71147246 SRX12190883 SRS10168720 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.94535 0.75289 0.20051 0.18779 0.84139 0.8646 0.74818 0.65269 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66092 66092 SRR15900246 SRX12190882 SRS10168719 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 2   strain:AB|isolate:C2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C2 tchenlab C2 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_5.8.IP_R1.fastq.gz DMSO_5.8.IP_R2.fastq.gz DMSO_5.8.Input_R1.fastq.gz DMSO_5.8.Input_R2.fastq.gz fastq fastq fastq fastq 12272849400.0 40909498.0 DMSO 5.8.IP R1.fastq.gz 0:150 1:150 A:2381041881;C:3673513092;G:3850518138;T:2295835815;N:71940474 150 150     2381041881 3673513092 3850518138 2295835815 71940474 SRX12190882 SRS10168719 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.88711 0.71046 0.18073 0.17436 0.84654 0.8674 0.76218 0.63257 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
66093 66093 SRR15900247 SRX12190881 SRS10168718 SRP337081 PRJNA763243 m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos PRJNA763243 Other This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14 which can be restored by AHR inhibitor CH or AHR knockdown. In addition EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos and these can be attenuated by enforced METTL14 overexpression. In conclusion AHR activated by PM2.5 significantly inhibits METTL14 expression which in turn disrupts heart development via oxidative stress and apoptosis resulting in heart defects in zebrafish embryos.         DMSO 1   strain:AB|isolate:C1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal                 RNA m6A methylation of zebrafish tchenlab C1 tchenlab C1 M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.     RIP-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina NovaSeq 6000   SRP337081   loader:fastq load.py DMSO_4.16.IP_R1.fastq.gz DMSO_4.16.IP_R2.fastq.gz DMSO_4.16.Input_R1.fastq.gz DMSO_4.16.Input_R2.fastq.gz fastq fastq fastq fastq 12900597000.0 43001990.0 DMSO 4.16.IP R1.fastq.gz 0:150 1:150 A:2517062962;C:3854768074;G:4032734290;T:2426295392;N:69736282 150 150     2517062962 3854768074 4032734290 2426295392 69736282 SRX12190881 SRS10168718 SRA1294636 Soochow University|Department of Toxicology, School of Public Health Soochow University 2 0.75605 0.5734 0.16268 0.14503 0.8714 0.89422 0.72976 0.64046 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming nebnext bulk unknown unknown   Unknown 2021-09-15 Larval Larval Undetermined Undetermined
68548 68548 SRR18056674 SRX14208687 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT6 6 6 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT6.R1.fq.gz SS3WT6.R2.fq.gz fastq fastq 7174164397.0 25400980.0 SS3WT6.R1.fq.gz 0:141.31 1:141.13 A:1934605412;C:1644763885;G:1664938935;T:1929811138;N:45027 141 141     1934605412 1644763885 1664938935 1929811138 45027 SRX14208687 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94928 0.94948 0.09187 0.09099 0.68765 0.68769 0.50435 0.50363 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68549 68549 SRR18056675 SRX14208686 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT5 5 5 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT5.R1.fq.gz SS3WT5.R2.fq.gz fastq fastq 7159028081.0 25133913.0 SS3WT5.R1.fq.gz 0:142.50 1:142.33 A:1905921436;C:1664337487;G:1683294939;T:1905427825;N:46394 142 142     1905921436 1664337487 1683294939 1905427825 46394 SRX14208686 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94917 0.95027 0.09384 0.09347 0.6594 0.65894 0.49218 0.49202 122 122 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68550 68550 SRR18056676 SRX14208685 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT4 4 4 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT4.R1.fq.gz SS3WT4.R2.fq.gz fastq fastq 6985092696.0 24360978.0 SS3WT4.R1.fq.gz 0:143.44 1:143.29 A:1858629258;C:1624045323;G:1642960060;T:1859412787;N:45268 143 143     1858629258 1624045323 1642960060 1859412787 45268 SRX14208685 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94221 0.94208 0.1047 0.1038 0.66231 0.66251 0.49213 0.49128 113 112 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68551 68551 SRR18056677 SRX14208684 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT3 3 3 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT3.R1.fq.gz SS3WT3.R2.fq.gz fastq fastq 6604271936.0 23189546.0 SS3WT3.R1.fq.gz 0:142.47 1:142.32 A:1765899330;C:1527534084;G:1543609939;T:1767186572;N:42011 142 142     1765899330 1527534084 1543609939 1767186572 42011 SRX14208684 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94017 0.94088 0.10254 0.10225 0.65163 0.65167 0.47798 0.47707 131 131 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68552 68552 SRR18056678 SRX14208683 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT2 2 2 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT2.R1.fq.gz SS3WT2.R2.fq.gz fastq fastq 6674317073.0 23265242.0 SS3WT2.R1.fq.gz 0:143.52 1:143.36 A:1768071045;C:1560492667;G:1576548690;T:1769161220;N:43451 143 143     1768071045 1560492667 1576548690 1769161220 43451 SRX14208683 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94677 0.9473 0.08956 0.08902 0.66559 0.66557 0.48058 0.48136 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68553 68553 SRR18056679 SRX14208682 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT1 1 1 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT1.R1.fq.gz SS3WT1.R2.fq.gz fastq fastq 6848211264.0 23787995.0 SS3WT1.R1.fq.gz 0:144.06 1:143.82 A:1825907736;C:1587014566;G:1607121352;T:1828122105;N:45505 144 143     1825907736 1587014566 1607121352 1828122105 45505 SRX14208682 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94226 0.94255 0.09053 0.08971 0.65807 0.65823 0.48525 0.48427 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined

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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");;