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run_metadata

54 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "Oligo-dT" and tissue_curation_coarse = "Digestive System"

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devstage_curation_coarse 3

devstage_curation 3

technology 2

experiment.platform 2

experiment.library_source 2

tissue_curation_coarse 1

  • Digestive System · 54 ✖

tissue_curation 1

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 54 ✖

experiment.library_layout 1

  • PAIRED · 54 ✖
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
24918 24918 SRR25594442 SRX21322829 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 2 1.fq Z 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-2_2.fq.gz Z-2_1.fq.gz fastq fastq 5621492400.0 18738308.0 Z 2 1.fq.gz 0:150 1:150 A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847 150 150     1483421677 1306378425 1338052121 1493618330 21847 SRX21322829 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94389 0.93819 0.03702 0.03621 0.71758 0.72423 0.43774 0.4558 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24919 24919 SRR25594443 SRX21322828 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 1 1.fq Z 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-1_2.fq.gz Z-1_1.fq.gz fastq fastq 6301274700.0 21004249.0 Z 1 1.fq.gz 0:150 1:150 A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450 150 150     1671253253 1458678359 1491311308 1680006330 25450 SRX21322828 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94339 0.93817 0.03831 0.03813 0.71752 0.72293 0.42611 0.43548 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24920 24920 SRR25594444 SRX21322827 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 3 1.fq K 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-3_2.fq.gz K-3_1.fq.gz fastq fastq 5519682000.0 18398940.0 K 3 1.fq.gz 0:150 1:150 A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289 150 150     1469946965 1270791684 1304075220 1474846842 21289 SRX21322827 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94356 0.93561 0.03986 0.03923 0.71877 0.72697 0.44771 0.44936 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24921 24921 SRR25594445 SRX21322826 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 2 1.fq K 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-2_1.fq.gz K-2_2.fq.gz fastq fastq 5808261300.0 19360871.0 K 2 1.fq.gz 0:150 1:150 A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660 150 150     1538012312 1343217111 1375887577 1551118640 25660 SRX21322826 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94469 0.94137 0.03929 0.03857 0.7175 0.71946 0.44395 0.44354 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24922 24922 SRR25594446 SRX21322825 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 3 1.fq ZP 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-3_1.fq.gz ZP-3_2.fq.gz fastq fastq 5397938100.0 17993127.0 ZP 3 1.fq.gz 0:150 1:150 A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855 150 150     1438191584 1244532731 1271700792 1443491138 21855 SRX21322825 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94839 0.94406 0.04345 0.04279 0.71719 0.72362 0.42772 0.4311 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24923 24923 SRR25594447 SRX21322824 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 2 1.fq ZP 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-2_1.fq.gz ZP-2_2.fq.gz fastq fastq 6062424900.0 20208083.0 ZP 2 1.fq.gz 0:150 1:150 A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752 150 150     1612595576 1398589726 1427536119 1623678727 24752 SRX21322824 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.95013 0.94657 0.04364 0.04342 0.71565 0.71908 0.44652 0.44832 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24924 24924 SRR25594448 SRX21322823 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 1 1.fq ZP 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-1_2.fq.gz ZP-1_1.fq.gz fastq fastq 6487607100.0 21625357.0 ZP 1 1.fq.gz 0:150 1:150 A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516 150 150     1728514584 1494175744 1521726756 1743164500 25516 SRX21322823 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94867 0.94432 0.04535 0.0449 0.71926 0.72348 0.43747 0.44661 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24925 24925 SRR25594449 SRX21322822 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 3 1.fq Z 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-3_1.fq.gz Z-3_2.fq.gz fastq fastq 8111204700.0 27037349.0 Z 3 1.fq.gz 0:150 1:150 A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125 150 150     2143712842 1879826122 1918517283 2169119328 29125 SRX21322822 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94485 0.94083 0.03886 0.03798 0.71362 0.71768 0.44066 0.44713 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24926 24926 SRR25594450 SRX21322821 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 1 1.fq K 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-1_1.fq.gz K-1_2.fq.gz fastq fastq 7164142200.0 23880474.0 K 1 1.fq.gz 0:150 1:150 A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789 150 150     1896647470 1661542391 1700422400 1905500150 29789 SRX21322821 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94635 0.94209 0.03738 0.03664 0.71961 0.72571 0.45014 0.44857 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
67005 67005 SRR16972425 SRX13163301 SRS11094637 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         MU 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:chs1 / |health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut MU 6M rep2 MU 6M rep2 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689     Daniorerio_6months_MU2-01T0003_good_1.fq.gz Daniorerio_6months_MU2-01T0003_good_2.fq.gz Daniorerio_6months_MU2_add-01T0003_good_1.fq.gz Daniorerio_6months_MU2_add-01T0003_good_2.fq.gz fastq fastq fastq fastq 26247918860.0 88200239.0 Daniorerio 6months MU2 01T0003 good 1.fq.gz 0:148.80 1:148.80 A:6706581059;C:6362908903;G:6430710510;T:6747581679;N:136709 148 148     6706581059 6362908903 6430710510 6747581679 136709 SRX13163301 SRS11094637 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.94119 0.94122 0.05124 0.05059 0.75043 0.75065 0.52934 0.53052 140 140 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-18 Adult Adult Gut Digestive System
67006 67006 SRR16972426 SRX13163300 SRS11094638 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 3M   breed:TU|age:3 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 10 15|death date:2020 10 15|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 3M rep2 WT 3M rep2 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_3months_WT2-T04_good_1.fq.gz Daniorerio_3months_WT2-T04_good_2.fq.gz fastq fastq 8467967054.0 28305387.0 Daniorerio 3months WT2 T04 good 1.fq.gz 0:149.58 1:149.58 A:2259351363;C:1963646091;G:1984749237;T:2259951700;N:268663 149 149     2259351363 1963646091 1984749237 2259951700 268663 SRX13163300 SRS11094638 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.92857 0.9274 0.07369 0.07329 0.7344 0.73598 0.52047 0.53156 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67007 67007 SRR16972427 SRX13163299 SRS11094638 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 3M   breed:TU|age:3 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 10 15|death date:2020 10 15|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 3M rep1 WT 3M rep1 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_3months_WT1-T03_good_1.fq.gz Daniorerio_3months_WT1-T03_good_2.fq.gz fastq fastq 7212592596.0 24118086.0 Daniorerio 3months WT1 T03 good 1.fq.gz 0:149.53 1:149.53 A:1928347826;C:1670886595;G:1685298858;T:1927833118;N:226199 149 149     1928347826 1670886595 1685298858 1927833118 226199 SRX13163299 SRS11094638 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.92847 0.92926 0.07508 0.07526 0.7402 0.74115 0.53069 0.52994 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67008 67008 SRR16972428 SRX13163298 SRS11094637 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         MU 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:chs1 / |health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut MU 6M rep1 MU 6M rep1 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689     Daniorerio_6months_MU1-01T0002_good_1.fq.gz Daniorerio_6months_MU1-01T0002_good_2.fq.gz Daniorerio_6months_MU1_add-01T0002_good_1.fq.gz Daniorerio_6months_MU1_add-01T0002_good_2.fq.gz fastq fastq fastq fastq 25069949786.0 84048581.0 Daniorerio 6months MU1 01T0002 good 1.fq.gz 0:149.14 1:149.14 A:6557923073;C:5921477753;G:5998862929;T:6591554621;N:131410 149 149     6557923073 5921477753 5998862929 6591554621 131410 SRX13163298 SRS11094637 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.92686 0.92635 0.04539 0.04507 0.74024 0.74111 0.5104 0.51793 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-18 Adult Adult Gut Digestive System
67009 67009 SRR16972429 SRX13163297 SRS11094636 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 6M rep5 WT 6M rep5 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_6months_WT5-T11_good_1.fq.gz Daniorerio_6months_WT5-T11_good_2.fq.gz fastq fastq 7033656400.0 23536846.0 Daniorerio 6months WT5 T11 good 1.fq.gz 0:149.42 1:149.42 A:1811251955;C:1673819413;G:1713312637;T:1835256740;N:15655 149 149     1811251955 1673819413 1713312637 1835256740 15655 SRX13163297 SRS11094636 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.93702 0.93617 0.05475 0.0541 0.74789 0.74752 0.54482 0.54579 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67010 67010 SRR16972430 SRX13163296 SRS11094636 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 6M rep4 WT 6M rep4 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_6months_WT4-T10_good_1.fq.gz Daniorerio_6months_WT4-T10_good_2.fq.gz fastq fastq 7012965398.0 23448817.0 Daniorerio 6months WT4 T10 good 1.fq.gz 0:149.54 1:149.54 A:1853320249;C:1629815005;G:1669888653;T:1859925598;N:15893 149 149     1853320249 1629815005 1669888653 1859925598 15893 SRX13163296 SRS11094636 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.9271 0.92565 0.07612 0.07593 0.73466 0.73649 0.51338 0.51974 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67011 67011 SRR16972431 SRX13163295 SRS11094636 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 6M rep3 WT 6M rep3 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689     Daniorerio_6months_WT3-02T0002_good_1.fq.gz Daniorerio_6months_WT3-02T0002_good_2.fq.gz Daniorerio_6months_WT3_add-02T0002_good_1.fq.gz Daniorerio_6months_WT3_add-02T0002_good_2.fq.gz fastq fastq fastq fastq 17759887004.0 59457706.0 Daniorerio 6months WT3 02T0002 good 1.fq.gz 0:149.35 1:149.35 A:4712859735;C:4120528947;G:4179191528;T:4747044398;N:262396 149 149     4712859735 4120528947 4179191528 4747044398 262396 SRX13163295 SRS11094636 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.94132 0.94052 0.05379 0.05353 0.76274 0.76301 0.53446 0.54191 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-18 Adult Adult Gut Digestive System
67012 67012 SRR16972432 SRX13163294 SRS11094636 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 6M rep2 WT 6M rep2 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689     Daniorerio_6months_WT2-02T0001_good_1.fq.gz Daniorerio_6months_WT2-02T0001_good_2.fq.gz Daniorerio_6months_WT2_add-02T0001_good_1.fq.gz Daniorerio_6months_WT2_add-02T0001_good_2.fq.gz fastq fastq fastq fastq 17304877338.0 58005868.0 Daniorerio 6months WT2 02T0001 good 1.fq.gz 0:149.16 1:149.16 A:4567317204;C:4029770990;G:4089916090;T:4617621274;N:251780 149 149     4567317204 4029770990 4089916090 4617621274 251780 SRX13163294 SRS11094636 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.9417 0.94125 0.04903 0.04882 0.74594 0.74675 0.52815 0.52403 140 140 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-18 Adult Adult Gut Digestive System
67013 67013 SRR16972433 SRX13163293 SRS11094636 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         WT 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2021 01 21|collection date:2021 07 09|death date:2021 07 09|genotype:wild type|health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut WT 6M rep1 WT 6M rep1 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689     Daniorerio_6months_WT1-01T0001_good_1.fq.gz Daniorerio_6months_WT1-01T0001_good_2.fq.gz Daniorerio_6months_WT1_add-01T0001_good_1.fq.gz Daniorerio_6months_WT1_add-01T0001_good_2.fq.gz fastq fastq fastq fastq 16602152324.0 55578781.0 Daniorerio 6months WT1 01T0001 good 1.fq.gz 0:149.36 1:149.36 A:4245434211;C:3997153641;G:4055895554;T:4303584997;N:83921 149 149     4245434211 3997153641 4055895554 4303584997 83921 SRX13163293 SRS11094636 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.94805 0.94713 0.03859 0.03827 0.7609 0.76021 0.52389 0.53306 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-18 Adult Adult Gut Digestive System
67014 67014 SRR16972434 SRX13163292 SRS11094635 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         MU 3M   breed:TU|age:3 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 10 15|death date:2020 10 15|genotype:chs1 / |health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut MU 3M rep2 MU 3M rep2 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_3months_MU2-T02_good_1.fq.gz Daniorerio_3months_MU2-T02_good_2.fq.gz fastq fastq 7319481642.0 24455109.0 Daniorerio 3months MU2 T02 good 1.fq.gz 0:149.65 1:149.65 A:1950119505;C:1698268609;G:1716794920;T:1954208020;N:90588 149 149     1950119505 1698268609 1716794920 1954208020 90588 SRX13163292 SRS11094635 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.91605 0.91629 0.07171 0.0721 0.73099 0.73277 0.51829 0.51094 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67015 67015 SRR16972435 SRX13163291 SRS11094635 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         MU 3M   breed:TU|age:3 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 10 15|death date:2020 10 15|genotype:chs1 / |health state:health|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut MU 3M rep1 MU 3M rep1 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_3months_MU1-T01_good_1.fq.gz Daniorerio_3months_MU1-T01_good_2.fq.gz fastq fastq 6689783730.0 22374730.0 Daniorerio 3months MU1 T01 good 1.fq.gz 0:149.49 1:149.49 A:1791825331;C:1543674432;G:1559586766;T:1794614998;N:82203 149 149     1791825331 1543674432 1559586766 1794614998 82203 SRX13163291 SRS11094635 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.89988 0.90023 0.07447 0.07414 0.73318 0.7347 0.52608 0.52855 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67016 67016 SRR16972436 SRX13163290 SRS11094634 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         SMU 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 12 29|death date:2020 12 29|genotype:chs1 / |health state:sick|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut SMU 6M rep2 SMU 6M rep2 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_6months_SMU2-T09_good_1.fq.gz Daniorerio_6months_SMU2-T09_good_2.fq.gz fastq fastq 6153057638.0 20567236.0 Daniorerio 6months SMU2 T09 good 1.fq.gz 0:149.58 1:149.58 A:1623915064;C:1438971834;G:1466951426;T:1623205362;N:13952 149 149     1623915064 1438971834 1466951426 1623205362 13952 SRX13163290 SRS11094634 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.89898 0.89771 0.08023 0.07995 0.715 0.71648 0.49782 0.48134 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
67017 67017 SRR16972437 SRX13163289 SRS11094634 SRP346689 PRJNA781427 RNA Seq analysis of wild type and chs1 / zebrafish gut PRJNA781427 Other To investigate the mRNA expression profiles in the intestine of wild type and chitin synthase 1 knock out chs1 / zebrafish extracted total RNA of intestine from samples of different ages to generate cDNA libraries and sequenced using Illumina NovaSeq 6000 system platform.         SMU 6M   breed:TU|age:6 mpf|dev stage:Adult|sex:not collected|tissue:Intestine|birth date:2020 07 08|collection date:2020 12 29|death date:2020 12 29|genotype:chs1 / |health state:sick|sample type:tissue sample|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult gut SMU 6M rep1 SMU 6M rep1 Adults Danio rerio were euthanized by MS 222 whole intestines were collected from the abdomen region. Total RNA was extracted using TRIzol Plus RNA Purification Kit. cDNA libraries were generated by Oligo dT for sequencing.     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP346689   loader:fastq load.py|options: doNotUseSharq allowEarlyFileEnd maxErrorCount=0 Daniorerio_6months_SMU1-T08_good_1.fq.gz Daniorerio_6months_SMU1-T08_good_2.fq.gz fastq fastq 6402267634.0 21457841.0 Daniorerio 6months SMU1 T08 good 1.fq.gz 0:149.18 1:149.18 A:1705727400;C:1483728129;G:1516588316;T:1696209255;N:14534 149 149     1705727400 1483728129 1516588316 1696209255 14534 SRX13163289 SRS11094634 SRA1330971 Sun Yat-sen University|School of Life Sciences Sun Yat-sen University 2 0.92502 0.92362 0.09504 0.09399 0.69323 0.69568 0.4847 0.48708 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-11-19 Adult Adult Gut Digestive System
70700 70700 SRR21457006 SRX17460727 SRS15014538 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Hepatized intestine in lbw S1 L002   isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 2|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf lbw mutant intestine LG S1 L002 aliquot 2 LG S1 L002 aliquot 2 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S1_LG_20200825NB_S1_L002_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L002_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L002_R2_001.fastq.gz fastq fastq fastq 14193607989.0 75901647.0 20200806 S1 LG 20200825NB S1 L002 I1 001.fastq.gz 0:8 1:28 2:151 A:3301648645;C:2611036971;G:2734265669;T:2814086798;N:110614 8 28 151   3301648645 2611036971 2734265669 2814086798 110614 SRX17460727 SRS15014538 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.91108   0.11686   0.85557   0.57466   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70701 70701 SRR21457007 SRX17460726 SRS15014537 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Hepatized intestine in lbw S1 L001   isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 1|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf lbw mutant intestine LG S1 L001 aliquot 1 LG S1 L001 aliquot 1 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S1_LG_20200825NB_S1_L001_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L001_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L001_R2_001.fastq.gz fastq fastq fastq 14182591632.0 75842736.0 20200806 S1 LG 20200825NB S1 L001 I1 001.fastq.gz 0:8 1:28 2:151 A:3299405296;C:2608368813;G:2735448901;T:2808939262;N:90864 8 28 151   3299405296 2608368813 2735448901 2808939262 90864 SRX17460726 SRS15014537 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.91027   0.11587   0.85587   0.72332   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70702 70702 SRR21457008 SRX17460725 SRS15014536 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Intestine in the WT S2 L004   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 4|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type intestine Gut S2 L004 aliquot 4 Gut S2 L004 aliquot 4 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S2_Gut_20200825NB_S2_L004_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L004_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L004_R2_001.fastq.gz fastq fastq fastq 16914022840.0 90449320.0 20200806 S2 Gut 20200825NB S2 L004 I1 001.fastq.gz 0:8 1:28 2:151 A:4133386049;C:3106166206;G:3057574159;T:3360630096;N:90810 8 28 151   4133386049 3106166206 3057574159 3360630096 90810 SRX17460725 SRS15014536 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.92139   0.0763   0.88294   0.43703   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70703 70703 SRR21457009 SRX17460724 SRS15014535 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Intestine in the WT S2 L003   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 3|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type intestine Gut S2 L003 aliquot 3 Gut S2 L003 aliquot 3 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S2_Gut_20200825NB_S2_L003_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L003_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L003_R2_001.fastq.gz fastq fastq fastq 16982190885.0 90813855.0 20200806 S2 Gut 20200825NB S2 L003 I1 001.fastq.gz 0:8 1:28 2:151 A:4147484891;C:3121909538;G:3068007254;T:3375339308;N:151114 8 28 151   4147484891 3121909538 3068007254 3375339308 151114 SRX17460724 SRS15014535 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.92489   0.07717   0.88264   0.74722   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70704 70704 SRR21457010 SRX17460723 SRS15014534 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Intestine in the WT S2 L002   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 2|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type intestine Gut S2 L002 aliquot 2 Gut S2 L002 aliquot 2 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S2_Gut_20200825NB_S2_L002_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L002_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L002_R2_001.fastq.gz fastq fastq fastq 16821098800.0 89952400.0 20200806 S2 Gut 20200825NB S2 L002 I1 001.fastq.gz 0:8 1:28 2:151 A:4111764153;C:3090100433;G:3032700332;T:3348115120;N:132362 8 28 151   4111764153 3090100433 3032700332 3348115120 132362 SRX17460723 SRS15014534 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.92867   0.07772   0.88162   0.75163   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70705 70705 SRR21457011 SRX17460722 SRS15014533 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Intestine in the WT S2 L001   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:intestine|aliquot:aliquot 1|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type intestine Gut S2 L001 aliquot 1 Gut S2 L001 aliquot 1 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S2_Gut_20200825NB_S2_L001_I1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L001_R1_001.fastq.gz 20200806_S2_Gut_20200825NB_S2_L001_R2_001.fastq.gz fastq fastq fastq 16838878760.0 90047480.0 20200806 S2 Gut 20200825NB S2 L001 I1 001.fastq.gz 0:8 1:28 2:151 A:4115908576;C:3092172269;G:3039279605;T:3349698554;N:110476 8 28 151   4115908576 3092172269 3039279605 3349698554 110476 SRX17460722 SRS15014533 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.92762   0.07664   0.88172   0.73829   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70708 70708 SRR21457014 SRX17460719 SRS15014530 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Hepatized intestine in lbw S1 L004   isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 4|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf lbw mutant intestine LG S1 L004 aliquot 4 LG S1 L004 aliquot 4 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S1_LG_20200825NB_S1_L004_I1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L004_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L004_R2_001.fastq.gz fastq fastq fastq 14467696881.0 77367363.0 20200806 S1 LG 20200825NB S1 L004 I1 001.fastq.gz 0:8 1:28 2:151 A:3365177661;C:2661264013;G:2793822598;T:2862129575;N:77966 8 28 151   3365177661 2661264013 2793822598 2862129575 77966 SRX17460719 SRS15014530 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90564   0.11415   0.85669   0.72469   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
70709 70709 SRR21457015 SRX17460718 SRS15014529 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Hepatized intestine in lbw S1 L003   isolate:lbw/cdx1b mutant|dev stage:6 dpf|sex:female and male|tissue:hepatized intestine|aliquot:aliquot 3|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf lbw mutant intestine LG S1 L003 aliquot 3 LG S1 L003 aliquot 3 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S1_LG_20200825NB_S1_L003_R1_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L003_R2_001.fastq.gz 20200806_S1_LG_20200825NB_S1_L003_I1_001.fastq.gz fastq fastq fastq 14438452138.0 77210974.0 20200806 S1 LG 20200825NB S1 L003 I1 001.fastq.gz 0:8 1:28 2:151 A:3354566334;C:2659200277;G:2787479629;T:2857478988;N:131846 8 28 151   3354566334 2659200277 2787479629 2857478988 131846 SRX17460718 SRS15014529 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90915   0.11415   0.85427   0.7235   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Gut Digestive System
74161 74161 SRR23576625 SRX19463432 SRS16856055 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M9   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut WT R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M9 M9 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M9_1.fq.gz M9_2.fq.gz fastq fastq 10791781600.0 107917816.0 M9 1.fq.gz 0:100 1:100 A:2848108353;C:2487301410;G:2561260439;T:2895111398;N:0 100 100     2848108353 2487301410 2561260439 2895111398 0 SRX19463432 SRS16856055 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95252   0.05974   0.79184   0.6274   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74162 74162 SRR23576626 SRX19463431 SRS16856054 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M8   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut WT R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M8 M8 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M8_1.fq.gz M8_2.fq.gz fastq fastq 10803624400.0 108036244.0 M8 1.fq.gz 0:100 1:100 A:2826927335;C:2516499907;G:2585204327;T:2874992831;N:0 100 100     2826927335 2516499907 2585204327 2874992831 0 SRX19463431 SRS16856054 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95494   0.06268   0.79139   0.60873   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74163 74163 SRR23576627 SRX19463430 SRS16856053 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M7   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut WT R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M7 M7 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M7_1.fq.gz M7_2.fq.gz fastq fastq 10794944600.0 107949446.0 M7 1.fq.gz 0:100 1:100 A:2822800001;C:2515936087;G:2583221720;T:2872986792;N:0 100 100     2822800001 2515936087 2583221720 2872986792 0 SRX19463430 SRS16856053 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95392   0.0552   0.78967   0.61766   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74164 74164 SRR23576628 SRX19463429 SRS16856052 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M6   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert with Cre R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M6 M6 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M6_1.fq.gz M6_2.fq.gz fastq fastq 10806717200.0 108067172.0 M6 1.fq.gz 0:100 1:100 A:2872422644;C:2476696362;G:2537205428;T:2920392766;N:0 100 100     2872422644 2476696362 2537205428 2920392766 0 SRX19463429 SRS16856052 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95383   0.06563   0.79293   0.63948   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74165 74165 SRR23576629 SRX19463428 SRS16856051 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M5   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert with Cre R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M5 M5 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M5_1.fq.gz M5_2.fq.gz fastq fastq 10553024000.0 105530240.0 M5 1.fq.gz 0:100 1:100 A:2756587901;C:2467885042;G:2531072385;T:2797478672;N:0 100 100     2756587901 2467885042 2531072385 2797478672 0 SRX19463428 SRS16856051 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95761   0.05754   0.79435   0.61791   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74166 74166 SRR23576630 SRX19463427 SRS16856048 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M4   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert with Cre R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M4 M4 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M4_1.fq.gz M4_2.fq.gz fastq fastq 10821109400.0 108211094.0 M4 1.fq.gz 0:100 1:100 A:2853720356;C:2500021520;G:2567460910;T:2899906614;N:0 100 100     2853720356 2500021520 2567460910 2899906614 0 SRX19463427 SRS16856048 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95171   0.0636   0.78644   0.61061   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74174 74174 SRR23576638 SRX19463419 SRS16856040 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M3   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert without xxx R3|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M3 M3 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M3_1.fq.gz M3_2.fq.gz fastq fastq 10811204400.0 108112044.0 M3 1.fq.gz 0:100 1:100 A:2826338851;C:2514522241;G:2594843889;T:2875499419;N:0 100 100     2826338851 2514522241 2594843889 2875499419 0 SRX19463419 SRS16856040 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95049   0.05611   0.79127   0.60997   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74185 74185 SRR23576649 SRX19463408 SRS16856031 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M2   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert without xxx R2|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M2 M2 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M2_1.fq.gz M2_2.fq.gz fastq fastq 10784874600.0 107848746.0 M2 1.fq.gz 0:100 1:100 A:2800268243;C:2532669517;G:2601088355;T:2850848485;N:0 100 100     2800268243 2532669517 2601088355 2850848485 0 SRX19463408 SRS16856031 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95513   0.05808   0.78171   0.60306   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
74186 74186 SRR23576650 SRX19463407 SRS16856030 SRP423783 PRJNA937311 Telomere elongation in the gut extends systemic healthspan of zebrafish PRJNA937311 Other Telomere shortening is a hallmark of aging and is counteracted by telomerase. zebrafish gut is one of the organs with the fastest rate of telomere decline. However whether telomere dependent aging of an individual organ the gut causes systemic aging remains unknown. Here we show that preventing telomere shortening in the gut through tissue specific telomerase expression rescues premature aging of tert / . Conclusively we show that gut specific telomerase expression extends lifespan of tert / by 40 % while ameliorating natural aging. Our work demonstrates that delaying telomere shortening in the gut is sufficient to systemically counteract aging in zebrafish.         M1   strain:AB|age:9 month|dev stage:adulte|sex:male|tissue:gut|biomaterial provider:EL MAI Mounir|birth date:2019/11/20|birth location:Nice France|treatment:gut tert without xxx R1|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult male gut M1 M1 RNA Seq of Danio rerio : adult male gut     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED BGISEQ BGISEQ-500   SRP423783     M1_1.fq.gz M1_2.fq.gz fastq fastq 10797666400.0 107976664.0 M1 1.fq.gz 0:100 1:100 A:2818869037;C:2522566664;G:2592727107;T:2863503592;N:0 100 100     2818869037 2522566664 2592727107 2863503592 0 SRX19463407 SRS16856030 SRA1593824 Sun Yat-sen University Cancer Center|State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Miguel Godinho Ferreira 1 0.95195   0.06111   0.78184   0.6129   100   B   usable mapping rate bgi bgi unknown poly_a unknown bulk unknown unknown   China 2023-02-21 Adult Adult Gut Digestive System
75099 75099 SRR24295703 SRX20091106 SRS17422802 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S3 S0hpt S26 L003 R1 001.fastq   strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 0 hpt 20201026 S3 S0hpt S26 L003 R1 001 20201026 S3 S0hpt S26 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 30 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S3_S0hpt_S26_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S26_L003_R2_001.fastq.gz fastq fastq 9523579187.0 53204353.0 20201026 S3 S0hpt S26 L003 R1 001.fastq.gz 0:28 1:151 A:2683643441;C:2130409626;G:2213828474;T:2495632325;N:65321 28 151     2683643441 2130409626 2213828474 2495632325 65321 SRX20091106 SRS17422802 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00736 0.92902 0.00193 0.10378 0.98815 0.81525 0.45394 0.60873 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75100 75100 SRR24295704 SRX20091105 SRS17422801 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S3 S0hpt S8 L004 R1 001.fastq   strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 0 hpt 20201026 S3 S0hpt S8 L004 R1 001 20201026 S3 S0hpt S8 L004 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 28 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S3_S0hpt_S8_L004_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L004_R2_001.fastq.gz fastq fastq 11268103342.0 62950298.0 20201026 S3 S0hpt S8 L004 R1 001.fastq.gz 0:28 1:151 A:3165223318;C:2522144425;G:2624994106;T:2955567304;N:174189 28 151     3165223318 2522144425 2624994106 2955567304 174189 SRX20091105 SRS17422801 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00779 0.92717 0.00206 0.1034 0.98776 0.81544 0.48375 0.57614 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75101 75101 SRR24295705 SRX20091104 SRS17422800 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S3 S0hpt S8 L003 R1 001.fastq   strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 0 hpt 20201026 S3 S0hpt S8 L003 R1 001 20201026 S3 S0hpt S8 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 26 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S3_S0hpt_S8_L003_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L003_R2_001.fastq.gz fastq fastq 11318791667.0 63233473.0 20201026 S3 S0hpt S8 L003 R1 001.fastq.gz 0:28 1:151 A:3185910303;C:2527965947;G:2631985020;T:2972741298;N:189099 28 151     3185910303 2527965947 2631985020 2972741298 189099 SRX20091104 SRS17422800 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00736 0.92879 0.00199 0.10456 0.98827 0.81643 0.49224 0.57699 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75102 75102 SRR24295706 SRX20091103 SRS17422798 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S3 S0hpt S8 L002 R1 001.fastq   strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 0 hpt 20201026 S3 S0hpt S8 L002 R1 001 20201026 S3 S0hpt S8 L002 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 24 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S3_S0hpt_S8_L002_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L002_R2_001.fastq.gz fastq fastq 11212565191.0 62640029.0 20201026 S3 S0hpt S8 L002 R1 001.fastq.gz 0:28 1:151 A:3151088961;C:2508604162;G:2610615892;T:2942050613;N:205563 28 151     3151088961 2508604162 2610615892 2942050613 205563 SRX20091103 SRS17422798 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00781 0.92808 0.00205 0.10455 0.98744 0.81489 0.50675 0.61614 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75103 75103 SRR24295707 SRX20091102 SRS17422799 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S3 S0hpt S8 L001 R1 001.fastq   strain:not applicable|dev stage:MTZ 0 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 0 hpt 20201026 S3 S0hpt S8 L001 R1 001 20201026 S3 S0hpt S8 L001 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 22 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S3_S0hpt_S8_L001_R1_001.fastq.gz 20201026_S3_S0hpt_S8_L001_R2_001.fastq.gz fastq fastq 11551003355.0 64530745.0 20201026 S3 S0hpt S8 L001 R1 001.fastq.gz 0:28 1:151 A:3248866155;C:2582279236;G:2687784274;T:3031856357;N:217333 28 151     3248866155 2582279236 2687784274 3031856357 217333 SRX20091102 SRS17422799 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00773 0.92693 0.00213 0.10378 0.98796 0.81458 0.48003 0.61476 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75104 75104 SRR24295708 SRX20091101 SRS17422797 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S1 BF S24 L003 R1 001.fastq   strain:not applicable|dev stage:7 dpf|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: BT 20201026 S1 BF S24 L003 R1 001 20201026 S1 BF S24 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 20 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S1_BF_S24_L003_R1_001.fastq.gz 20201026_S1_BF_S24_L003_R2_001.fastq.gz fastq fastq 16924465573.0 94550087.0 20201026 S1 BF S24 L003 R1 001.fastq.gz 0:28 1:151 A:4886602093;C:3870736671;G:3757579268;T:4409430253;N:117288 28 151     4886602093 3870736671 3757579268 4409430253 117288 SRX20091101 SRS17422797 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00762 0.94081 0.00182 0.08601 0.99194 0.85859 0.65178 0.72774 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Larval Larval Gut Digestive System
75105 75105 SRR24295709 SRX20091100 SRS17422796 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S1 BF S6 L004 R1 001.fastq   strain:not applicable|dev stage:7 dpf|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: BT 20201026 S1 BF S6 L004 R1 001 20201026 S1 BF S6 L004 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 18 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S1_BF_S6_L004_R1_001.fastq.gz 20201026_S1_BF_S6_L004_R2_001.fastq.gz fastq fastq 9841936415.0 54982885.0 20201026 S1 BF S6 L004 R1 001.fastq.gz 0:28 1:151 A:2834721114;C:2252697251;G:2189518877;T:2564845090;N:154083 28 151     2834721114 2252697251 2189518877 2564845090 154083 SRX20091100 SRS17422796 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00786 0.93893 0.00204 0.08672 0.99178 0.85886 0.66488 0.71597 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Larval Larval Gut Digestive System
75106 75106 SRR24295710 SRX20091099 SRS17422795 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S1 BF S6 L003 R1 001.fastq   strain:not applicable|dev stage:7 dpf|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: BT 20201026 S1 BF S6 L003 R1 001 20201026 S1 BF S6 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 16 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S1_BF_S6_L003_R1_001.fastq.gz 20201026_S1_BF_S6_L003_R2_001.fastq.gz fastq fastq 9794371998.0 54717162.0 20201026 S1 BF S6 L003 R1 001.fastq.gz 0:28 1:151 A:2825540725;C:2236862920;G:2175038375;T:2556767328;N:162650 28 151     2825540725 2236862920 2175038375 2556767328 162650 SRX20091099 SRS17422795 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00746 0.9385 0.00178 0.08677 0.99226 0.8621 0.68194 0.72039 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Larval Larval Gut Digestive System
75107 75107 SRR24295711 SRX20091098 SRS17422794 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S2 S48hpt S25 L003 R1 001.fastq   strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 9|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S25 L003 R1 001 20201026 S2 S48hpt S25 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 40 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S25_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S25_L003_R2_001.fastq.gz fastq fastq 14964717009.0 83601771.0 20201026 S2 S48hpt S25 L003 R1 001.fastq.gz 0:28 1:151 A:4042811725;C:3465477701;G:3602852950;T:3853470560;N:104073 28 151     4042811725 3465477701 3602852950 3853470560 104073 SRX20091098 SRS17422794 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00811 0.9409 0.00196 0.08687 0.98922 0.85001 0.51973 0.65526 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75108 75108 SRR24295712 SRX20091097 SRS17422793 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S2 S48hpt S7 L004 R1 001.fastq   strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 7|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S7 L004 R1 001 20201026 S2 S48hpt S7 L004 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 38 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L004_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L004_R2_001.fastq.gz fastq fastq 10669333843.0 59605217.0 20201026 S2 S48hpt S7 L004 R1 001.fastq.gz 0:28 1:151 A:2876329901;C:2471017739;G:2573143323;T:2748679474;N:163406 28 151     2876329901 2471017739 2573143323 2748679474 163406 SRX20091097 SRS17422793 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00841 0.93868 0.00188 0.08847 0.98879 0.85149 0.54358 0.6538 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75109 75109 SRR24295713 SRX20091096 SRS17422791 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S2 S48hpt S7 L003 R1 001.fastq   strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 5|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S7 L003 R1 001 20201026 S2 S48hpt S7 L003 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 36 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L003_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L003_R2_001.fastq.gz fastq fastq 10613956434.0 59295846.0 20201026 S2 S48hpt S7 L003 R1 001.fastq.gz 0:28 1:151 A:2867387827;C:2453215650;G:2555390367;T:2737785596;N:176994 28 151     2867387827 2453215650 2555390367 2737785596 176994 SRX20091096 SRS17422791 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00804 0.93909 0.00204 0.09014 0.98912 0.85289 0.53052 0.65123 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75110 75110 SRR24295714 SRX20091095 SRS17422792 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S2 S48hpt S7 L002 R1 001.fastq   strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S7 L002 R1 001 20201026 S2 S48hpt S7 L002 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 34 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L002_R1_001.fastq.gz 20201026_S2_S48hpt_S7_L002_R2_001.fastq.gz fastq fastq 10590029325.0 59162175.0 20201026 S2 S48hpt S7 L002 R1 001.fastq.gz 0:28 1:151 A:2855935581;C:2451968029;G:2552761582;T:2729169108;N:195025 28 151     2855935581 2451968029 2552761582 2729169108 195025 SRX20091095 SRS17422792 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00831 0.93901 0.00202 0.0879 0.98942 0.85072 0.5438 0.66125 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75111 75111 SRR24295715 SRX20091094 SRS17422790 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S2 S48hpt S7 L001 R1 001.fastq   strain:not applicable|dev stage:MTZ 48 hpt|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: MTZ 48 hpt 20201026 S2 S48hpt S7 L001 R1 001 20201026 S2 S48hpt S7 L001 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 32 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S2_S48hpt_S7_L001_R2_001.fastq.gz 20201026_S2_S48hpt_S7_L001_R1_001.fastq.gz fastq fastq 10843243262.0 60576778.0 20201026 S2 S48hpt S7 L001 R1 001.fastq.gz 0:28 1:151 A:2926797989;C:2508866130;G:2611743790;T:2795632661;N:202692 28 151     2926797989 2508866130 2611743790 2795632661 202692 SRX20091094 SRS17422790 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.00842 0.93796 0.00207 0.08873 0.98906 0.85204 0.53927 0.66266 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Undetermined Undetermined Gut Digestive System
75112 75112 SRR24295716 SRX20091093 SRS17422789 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S1 BF S6 L002 R1 001.fastq   strain:not applicable|dev stage:7 dpf|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 3|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: BT 20201026 S1 BF S6 L002 R1 001 20201026 S1 BF S6 L002 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 14 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S1_BF_S6_L002_R1_001.fastq.gz 20201026_S1_BF_S6_L002_R2_001.fastq.gz fastq fastq 9768359897.0 54571843.0 20201026 S1 BF S6 L002 R1 001.fastq.gz 0:28 1:151 A:2814406235;C:2235216093;G:2171625577;T:2546932148;N:179844 28 151     2814406235 2235216093 2171625577 2546932148 179844 SRX20091093 SRS17422789 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.008 0.93971 0.0019 0.08743 0.9917 0.85786 0.68112 0.70636 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Larval Larval Gut Digestive System
75113 75113 SRR24295717 SRX20091092 SRS17422788 SRP434294 PRJNA961336 Single cell transcriptome sequence of intestinal regeneration in zebrafish PRJNA961336 Other The jejunal regeneration is achieved by ileal enterocytes migration and transdifferentiation. To characterize the change of intestinal cell types and molecule mechanism we describe intestinal regeneration and performed scRNA seq to explore mechanism of migration and transdifferentiation.         20201026 S1 BF S6 L001 R1 001.fastq   strain:not applicable|dev stage:7 dpf|sex:pooled male and female|tissue:intestine|collection date:2020 10 26|geo loc name:China:Chongqing|replicate:replicate 1|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish intestine: BT 20201026 S1 BF S6 L001 R1 001 20201026 S1 BF S6 L001 R1 001 Single Cell 3 Gene Expression libraries comprise standard Illumina paired end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1 while 8 bp sample index sequences are incorporated as the sample index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI. Sequencing these libraries produce a standard Illumina BCL data output folder.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP434294     20201026_S1_BF_S6_L001_R1_001.fastq.gz 20201026_S1_BF_S6_L001_R2_001.fastq.gz fastq fastq 9991870216.0 55820504.0 20201026 S1 BF S6 L001 R1 001.fastq.gz 0:28 1:151 A:2880135309;C:2284287656;G:2221082847;T:2606178043;N:186361 28 151     2880135309 2284287656 2221082847 2606178043 186361 SRX20091092 SRS17422788 SRA1626787 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 2 0.008 0.93771 0.00184 0.08853 0.99159 0.85926 0.65177 0.72412 28 151 T B sc-like readlen illumina novaseq_era unknown poly_a trueseq sc single_cell_droplet 10x   China 2023-04-25 Larval Larval Gut Digestive 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");;