RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

437 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Liver and Biliary System"

✎ View and edit SQL

This data as json, CSV (advanced)

experiment.library_selection 6

devstage_curation_coarse 6

devstage_curation 5

experiment.platform 4

experiment.library_strategy 3

tissue_curation_coarse 1

  • Liver and Biliary System · 437 ✖

tissue_curation 1

technology 1

  • unknown · 437 ✖

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 437 ✖
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
171 171 DRR075399 DRX069313 DRS075494 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The liver of control fish 7dpf Control liver SAMD00065413   sample name:3 control liver 150701 Hiseq3A l3 019|tissue type:Liver                 Illumina HiSeq 2500 sequencing of SAMD00065413 DRX069313 Control liver 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065413       951579036.0 26432751.0 DRR075399 0:36 A:231570583;C:228182815;G:227223430;T:264569214;N:32994 36       231570583 228182815 227223430 264569214 32994 DRX069313 DRS075494 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.8903   0.08667   0.7236   0.51557   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Liver Liver and Biliary System
8104 8104 ERR2455366 ERX2474426 ERS2327331 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 4 SAMEA104725948 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 4 s Sample 4 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:overfeeding RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 OF-4_H7MWNALXX_L6_1.fq.gz fastq 4961276550.0 33075177.0 E MTAB 6636:Sample 4 0:150 1:0 A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133 150 0     1349413168 1135314970 1137935563 1338034716 578133 ERX2474426 ERS2327331 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.90787   0.11999   0.66123   0.49072   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8105 8105 ERR2455365 ERX2474425 ERS2327330 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 3 SAMEA104725947 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 3 s Sample 3 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:fructose RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Fru-3_H7MWNALXX_L5_1.fq.gz fastq 5858273250.0 39055155.0 E MTAB 6636:Sample 3 0:150 1:0 A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243 150 0     1580150663 1353221682 1355865524 1568428138 607243 ERX2474425 ERS2327330 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91505   0.11036   0.65985   0.48443   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8106 8106 ERR2455364 ERX2474424 ERS2327329 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 2 SAMEA104725946 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 2 s Sample 2 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:cholesterol RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Cho-2_H7MWNALXX_L5_1.fq.gz fastq 5636304900.0 37575366.0 E MTAB 6636:Sample 2 0:150 1:0 A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169 150 0     1526862069 1295343770 1298751994 1514766898 580169 ERX2474424 ERS2327329 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91032   0.11644   0.66649   0.47766   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8107 8107 ERR2455363 ERX2474423 ERS2327328 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 1 SAMEA104725945 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 1 s Sample 1 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:control RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 ND-1_H7MWNALXX_L5_1.fq.gz fastq 5197165350.0 34647769.0 E MTAB 6636:Sample 1 0:150 1:0 A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690 150 0     1430911816 1174811274 1175616551 1415284019 541690 ERX2474423 ERS2327328 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.89838   0.13883   0.66129   0.48467   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
31986 31986 SRR28894021 SRX24452441 SRS21206092 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 4   strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 4 8 8 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-4 fastq 4367010000.0 29113400.0 elovl2 4.gz 0:150 A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734 150       1161921878 1015107709 1012841192 1177020487 118734 SRX24452441 SRS21206092 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31987 31987 SRR28894022 SRX24452440 SRS21206091 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 3   strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 3 7 7 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-3 fastq 5125533150.0 34170221.0 elovl2 3.gz 0:150 A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776 150       1365645170 1189846405 1184721703 1385180096 139776 SRX24452440 SRS21206091 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31988 31988 SRR28894023 SRX24452439 SRS21206090 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 2   strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 2 6 6 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-2 fastq 3261375750.0 21742505.0 elovl2 2.gz 0:150 A:878478836;C:747963062;G:743760185;T:891083235;N:90432 150       878478836 747963062 743760185 891083235 90432 SRX24452439 SRS21206090 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31989 31989 SRR28894024 SRX24452438 SRS21206089 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         elovl2 1   strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 elovl2 1 5 5 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     elovl2-1 fastq 3629422950.0 24196153.0 elovl2 1.gz 0:150 A:974034477;C:836070594;G:831068189;T:988151010;N:98680 150       974034477 836070594 831068189 988151010 98680 SRX24452438 SRS21206089 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31990 31990 SRR28894025 SRX24452437 SRS21206088 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 4   strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 4 4 4 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-4 fastq 4037472900.0 26916486.0 WT 4.gz 0:150 A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413 150       1083383010 932278459 925831402 1095868616 111413 SRX24452437 SRS21206088 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31991 31991 SRR28894026 SRX24452436 SRS21206087 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 3   strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 3 3 3 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-3 fastq 3651994200.0 24346628.0 WT 3.gz 0:150 A:978819903;C:844506880;G:836704943;T:991863415;N:99059 150       978819903 844506880 836704943 991863415 99059 SRX24452436 SRS21206087 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31992 31992 SRR28894027 SRX24452435 SRS21206086 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 2   strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 2 2 2 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-2 fastq 3845338950.0 25635593.0 WT 2.gz 0:150 A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950 150       1033991995 885977441 878907105 1046356459 105950 SRX24452435 SRS21206086 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
31993 31993 SRR28894028 SRX24452434 SRS21206085 SRP505663 PRJNA1107798 liver PRJNA1107798 Other wt and elovl2 mutant liver         WT 1   strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 WT 1 1 1 liver     RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq X   SRP505663     WT-1 fastq 3756883050.0 25045887.0 WT 1.gz 0:150 A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839 150       1005244721 868304979 865360007 1017811504 161839 SRX24452434 SRS21206085 SRA1858809 Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology Chinese Academy of Sciences (CAS)                       B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   China 2024-05-04 Undetermined Undetermined Liver Liver and Biliary System
34958 34958 SRR32588715 SRX27895236 SRS24266238 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F L22   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Iso Seq RNA from liver C2 F2 F L22 C2 F2 F L22 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m64467e_240816_172726.hifi_reads.flnc.fastq.gz fastq 15103018596.0 3471157.0 m64467e 240816 172726.hifi reads.flnc.fastq.gz 0:4351.00 A:4102928612;C:3526979790;G:3455927740;T:4017182454;N:0 4351       4102928612 3526979790 3455927740 4017182454 0 SRX27895236 SRS24266238 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Liver Liver and Biliary System
34959 34959 SRR32588716 SRX27895235 SRS24266237 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 F L21   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Liver|BioSampleModel:Model organism or animal                 Iso Seq RNA from liver C2 F2 F L21 C2 F2 F L21 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240913_130745_s1.skera.flnc.fastq.gz fastq 91129501236.0 45094963.0 m84270 240913 130745 s1.skera.flnc.fastq.gz 0:2020.84 A:25808290124;C:20578070676;G:20740793271;T:24002347165;N:0 2020       25808290124 20578070676 20740793271 24002347165 0 SRX27895235 SRS24266237 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Liver Liver and Biliary System
34969 34969 SRR32588726 SRX27895225 SRS24266223 SRP568323 PRJNA1232602 Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains PRJNA1232602 Other In this study Iso Seq was performed on different zebrafish body organs enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues including the brain testis liver eye muscle ovary inner ear and kidney to identify novel isoforms tissue specific transcripts and alternative splicing events. We also made available the Iso Seq data from embryos from different time points hpf 0 6 12 and 24. This dataset enhances gene annotation improves reference genome annotations and provides insights into zebrafish organ specific gene expression.       Iso Seq RNA from Danio rerio C2 F2 M L   strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:liver|BioSampleModel:Model organism or animal                 Iso Seq RNA from liver C2 F2 M L C2 F2 M L The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     m84270_240911_170652_s2.skera.flnc.fastq.gz fastq 103288926144.0 58528654.0 m84270 240911 170652 s2.skera.flnc.fastq.gz 0:1764.76 A:30548263427;C:22289732504;G:23327561779;T:27123368434;N:0 1764       30548263427 22289732504 23327561779 27123368434 0 SRX27895225 SRS24266223 SRA2089085 National Human Genome Research Institute|Translational and Functional Genomics Branch National Human Genome Research Institute National Human Genome Research Institute                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Liver Liver and Biliary System
36336 36336 SRR390721 SRX112005 SRS282726 SRP009863 PRJNA151317 A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver GSE34493 Transcriptome Analysis We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.       mRNA from HBx+HCP transgenic line GSM850201   source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver mRNA from HBx+HCP transgenic line HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. zebrafish liver Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver GSM850201 GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq GSM850201 1 GSM850201: mRNA from HBx+HCP transgenic line 1   GEO Accession:GSM850201 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009863     HBx+HCP.qual HBx+HCP.csfasta SOLiD_native SOLiD_native 3946087000.0 78921740.0 GSM850201 r1 0:50 0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394 50                 SRX112005 SRS282726 SRA048698 GEO Institute of Cellular and Organismic Biology, Academia Sinica 1 0.71816   0.05681   0.91727   0.25279   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Taiwan 2011-12-16 Undetermined Adult Liver Liver and Biliary System
36337 36337 SRR390720 SRX112004 SRS282725 SRP009863 PRJNA151317 A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver GSE34493 Transcriptome Analysis We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.       mRNA from HCP transgenic line GSM850200   source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver mRNA from HCP transgenic line HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. zebrafish liver Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. phenotype:n1|strain:HCP transgenic|tissue:liver GSM850200 GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq GSM850200 1 GSM850200: mRNA from HCP transgenic line 1   GEO Accession:GSM850200 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009863     HCP.qual HCP.csfasta SOLiD_native SOLiD_native 4104044600.0 82080892.0 GSM850200 r1 0:50 0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070 50                 SRX112004 SRS282725 SRA048698 GEO Institute of Cellular and Organismic Biology, Academia Sinica 1 0.70132   0.05286   0.94422   0.26785   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Taiwan 2011-12-16 Undetermined Adult Liver Liver and Biliary System
36338 36338 SRR390719 SRX112003 SRS282724 SRP009863 PRJNA151317 A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver GSE34493 Transcriptome Analysis We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.       mRNA from HBx transgenic line GSM850199   source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver mRNA from HBx transgenic line HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. zebrafish liver Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. phenotype:n1|strain:HBx transgenic|tissue:liver GSM850199 GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq GSM850199 1 GSM850199: mRNA from HBx transgenic line 1   GEO Accession:GSM850199 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009863     HBx.qual HBx.csfasta SOLiD_native SOLiD_native 3783924950.0 75678499.0 GSM850199 r1 0:50 0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987 50                 SRX112003 SRS282724 SRA048698 GEO Institute of Cellular and Organismic Biology, Academia Sinica 1 0.70675   0.04174   0.94146   0.22954   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Taiwan 2011-12-16 Undetermined Adult Liver Liver and Biliary System
36339 36339 SRR390718 SRX112002 SRS282723 SRP009863 PRJNA151317 A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver GSE34493 Transcriptome Analysis We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.       mRNA from AB strain GSM850198   source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver mRNA from AB strain WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. zebrafish liver Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. phenotype:n1|strain:AB|tissue:liver GSM850198 GSM850198: mRNA from AB strain; Danio rerio; RNA Seq GSM850198 1 GSM850198: mRNA from AB strain 1   GEO Accession:GSM850198 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP009863     WT.csfasta WT.qual SOLiD_native SOLiD_native 5129652800.0 102593056.0 GSM850198 r1 0:50 0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426 50                 SRX112002 SRS282723 SRA048698 GEO Institute of Cellular and Organismic Biology, Academia Sinica 1 0.73072   0.04843   0.95574   0.21796   50   B   usable mapping rate legacy early full_length random_priming unknown bulk unknown unknown   Taiwan 2011-12-16 Undetermined Adult Liver Liver and Biliary System
36506 36506 SRR566696 SRX185761 SRS361914 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: liver tumor M+D+ GSM1000561: M+D+ 2 GSM1000561   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline M+D+ 2 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor M+D+ Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline GSM1000561 GSM1000561: M+D+ 2; Danio rerio; RNA Seq GSM1000561 1   1   GEO Accession:GSM1000561 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M+D+_2_QV.qual M+D+_2.csfasta SOLiD_native SOLiD_native 1493416960.0 42669056.0 GSM1000561 r1 0:35 0:377247910;1:348861020;2:522134600;3:237405266;.:7768164 35                 SRX185761 SRS361914 SRA058618 GEO National University of Singapore 1 0.06244   0.00306   0.99567   0.34618   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36507 36507 SRR566695 SRX185760 SRS361913 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: liver tumor M+D+ GSM1000560: M+D+ 1 GSM1000560   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline M+D+ 1 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor M+D+ Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline GSM1000560 GSM1000560: M+D+ 1; Danio rerio; RNA Seq GSM1000560 1   1   GEO Accession:GSM1000560 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680         1291539515.0 36901129.0 GSM1000560 r1 0:35 0:266006021;1:328523841;2:440474617;3:254266912;.:2268124 35                 SRX185760 SRS361913 SRA058618 GEO National University of Singapore 1 0.10629   0.0044   0.99239   0.31953   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36508 36508 SRR566694 SRX185759 SRS361912 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M D+ GSM1000559: M D+ 2 GSM1000559   genotype:wildtype|tissue:liver|treatment:doxycycline M D+ 2 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M D+ Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:wildtype|tissue:liver|treatment:doxycycline GSM1000559 GSM1000559: M D+ 2; Danio rerio; RNA Seq GSM1000559 1   1   GEO Accession:GSM1000559 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M-D+_2_QV.qual SOLiD_native 1438423910.0 41097826.0 GSM1000559 r1 0:35 0:353104627;1:349496969;2:433338629;3:275089557;.:27394128 35                 SRX185759 SRS361912 SRA058618 GEO National University of Singapore 1 0.04748   0.00442   0.99425   0.53794   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36509 36509 SRR566693 SRX185758 SRS361911 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M D+ GSM1000558: M D+ 1 GSM1000558   genotype:wildtype|tissue:liver|treatment:doxycycline M D+ 1 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M D+ Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:wildtype|tissue:liver|treatment:doxycycline GSM1000558 GSM1000558: M D+ 1; Danio rerio; RNA Seq GSM1000558 1   1   GEO Accession:GSM1000558 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M-D+_1.csfasta SOLiD_native 1284638285.0 36703951.0 GSM1000558 r1 0:35 0:328871758;1:317693850;2:402981931;3:233637468;.:1453278 35                 SRX185758 SRS361911 SRA058618 GEO National University of Singapore 1 0.10539   0.00562   0.99141   0.37635   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36510 36510 SRR566692 SRX185757 SRS361910 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M+D GSM1000557: M+D 2 GSM1000557   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 M+D 2 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M+D Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 GSM1000557 GSM1000557: M+D 2; Danio rerio; RNA Seq GSM1000557 1   1   GEO Accession:GSM1000557 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M+D-_2_QV.qual SOLiD_native 1404966080.0 40141888.0 GSM1000557 r1 0:35 0:371691603;1:354481639;2:405221861;3:271978812;.:1592165 35                 SRX185757 SRS361910 SRA058618 GEO National University of Singapore 1 0.07869   0.00455   0.99253   0.51508   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36511 36511 SRR566691 SRX185756 SRS361909 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M+D GSM1000556: M+D 1 GSM1000556   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 M+D 1 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M+D Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1 GSM1000556 GSM1000556: M+D 1; Danio rerio; RNA Seq GSM1000556 1   1   GEO Accession:GSM1000556 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M+D-_1_QV.qual M+D-_1.csfasta SOLiD_native SOLiD_native 1286706820.0 36763052.0 GSM1000556 r1 0:35 0:252864341;1:338709089;2:436928155;3:256235022;.:1970213 35                 SRX185756 SRS361909 SRA058618 GEO National University of Singapore 1 0.12399   0.00617   0.98752   0.50351   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36512 36512 SRR566690 SRX185755 SRS361908 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M D GSM1000555: M D 2 GSM1000555   genotype:wildtype|tissue:liver|treatment:n1 M D 2 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M D Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:wildtype|tissue:liver|treatment:n1 GSM1000555 GSM1000555: M D 2; Danio rerio; RNA Seq GSM1000555 1   1   GEO Accession:GSM1000555 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M-D-_2_QV.qual M-D-_2.csfasta SOLiD_native SOLiD_native 1337952770.0 38227222.0 GSM1000555 r1 0:35 0:391863829;1:347720340;2:312814682;3:283542736;.:2011183 35                 SRX185755 SRS361908 SRA058618 GEO National University of Singapore 1 0.04605   0.00365   0.99494   0.51825   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
36513 36513 SRR566689 SRX185754 SRS361907 SRP015680 PRJNA174800 Transcriptomic analyses of Myc induced zebrafish liver cancer GSE40745 Transcriptome Analysis To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.   pubmed:23038063 source: control liver M D GSM1000554: M D 1 GSM1000554   genotype:wildtype|tissue:liver|treatment:n1 M D 1 The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver M D Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day. Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype:wildtype|tissue:liver|treatment:n1 GSM1000554 GSM1000554: M D 1; Danio rerio; RNA Seq GSM1000554 1   1   GEO Accession:GSM1000554 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP015680     M-D-_1.csfasta SOLiD_native 1395143680.0 39861248.0 GSM1000554 r1 0:35 0:439852883;1:355203725;2:298639546;3:299770820;.:1676706 35                 SRX185754 SRS361907 SRA058618 GEO National University of Singapore 1 0.02094   0.00123   0.99784   0.58426   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2012-09-10 Larval Larval Liver Liver and Biliary System
37108 37108 SRR924082 SRX316721 SRS472258 SRP026400 PRJNA210007 Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver GSE48427 Transcriptome Analysis In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.   pubmed:24176670;pubmed:23922661   H2O treated zebrafish liver GSM1177837   source name:liver control|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control H2O treated zebrafish liver The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM. liver control 3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control GSM1177837 GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq GSM1177837   1 Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. GEO Accession:GSM1177837 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP026400     solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual SOLiD_native SOLiD_native 477311205.0 13637463.0 GSM1177837 r1 0:35 0:176467601;1:101093405;2:105775125;3:93265462;.:709612 35                 SRX316721 SRS472258 SRA091803 GEO National University of Singapore 1 0.02019   0.01385   0.9973   0.64062   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-06-28 Adult Adult Liver Liver and Biliary System
37109 37109 SRR924081 SRX316720 SRS454027 SRP026400 PRJNA210007 Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver GSE48427 Transcriptome Analysis In the present study we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure including oxidation reduction translation iron ion transport cell redox and homeostasis as well as related pathways in metabolism and diseases. Furthermore as there are currently no biomarker genes available for predicting arsenic exposure we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.   pubmed:24176670;pubmed:23922661   Arsenic treated zebrafish liver GSM1177836   source name:liver arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium Arsenic treated zebrafish liver The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI RefSeq accession and expression levels in TPM. liver arsenic 3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.   genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium GSM1177836 GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq GSM1177836   1 Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol. GEO Accession:GSM1177836 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP026400     solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta SOLiD_native SOLiD_native 477279215.0 13636549.0 GSM1177836 r1 0:35 0:135280436;1:121477647;2:102046207;3:117826846;.:648079 35                 SRX316720 SRS454027 SRA091803 GEO National University of Singapore 1 0.0161   0.00302   0.99334   0.51629   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-06-28 Adult Adult Liver Liver and Biliary System
37130 37130 SRR952910 SRX335554 SRS470625 SRP028848 PRJNA215326 Transcriptomic analyses of TCDD treated zebrafish liver GSE49915 Transcriptome Analysis To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system   pubmed:24204792   DMSO GSM1209643   source name:liver|tissue:liver|genotype:wildtype sibling|treatment:DMSO DMSO The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM. liver 3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:wildtype sibling|treatment:DMSO GSM1209643 GSM1209643: DMSO; Danio rerio; RNA Seq GSM1209643   1 Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1209643 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP028848     solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual SOLiD_native SOLiD_native 409327205.0 11695063.0 GSM1209643 r1 0:35 0:136723730;1:95263220;2:87949986;3:88818989;.:571280 35                 SRX335554 SRS470625 SRA098000 GEO National University of Singapore 1 0.01735   0.00647   0.9946   0.51324   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-08-15 Adult Adult Liver Liver and Biliary System
37131 37131 SRR952909 SRX335553 SRS470624 SRP028848 PRJNA215326 Transcriptomic analyses of TCDD treated zebrafish liver GSE49915 Transcriptome Analysis To fully understand molecular toxicity of TCDD in an in vivo animal model adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes 10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle endocrine disruptors signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system   pubmed:24204792   TCDD GSM1209642   source name:liver|tissue:liver|genotype:wildtype sibling|treatment:TCDD TCDD The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM. liver 3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:wildtype sibling|treatment:TCDD GSM1209642 GSM1209642: TCDD; Danio rerio; RNA Seq GSM1209642   1 Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1209642 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP028848     solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta SOLiD_native SOLiD_native 627514895.0 17928997.0 GSM1209642 r1 0:35 0:214639659;1:142538233;2:131819822;3:137625000;.:892181 35                 SRX335553 SRS470624 SRA098000 GEO National University of Singapore 1 0.01773   0.00917   0.99646   0.56398   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-08-15 Adult Adult Liver Liver and Biliary System
37217 37217 SRR1035240 SRX381137 SRS505529 SRP033231 PRJNA229468 Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma GSE52605 Transcriptome Analysis UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish cultured cells and human tumors we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.   pubmed:24486181   mCherry cntr2 GSM1272461   source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf mCherry cntr2 Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies. Zebrafish 5 dpf liver   Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends.   genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf GSM1272461 GSM1272461: mCherry cntr2; Danio rerio; RNA Seq GSM1272461   1 Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends. GEO Accession:GSM1272461 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP033231     mCherry_cntr2.fastq.gz fastq 2132003100.0 21320031.0 GSM1272461 r1 0:100 A:536532013;C:533562250;G:522685362;T:536641910;N:2581565 100       536532013 533562250 522685362 536641910 2581565 SRX381137 SRS505529 SRA111986 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.88347   0.04357   0.81964   0.52384   100   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2013-11-21 Larval Larval Liver Liver and Biliary System
37218 37218 SRR1035239 SRX381136 SRS505528 SRP033231 PRJNA229468 Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma GSE52605 Transcriptome Analysis UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish cultured cells and human tumors we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.   pubmed:24486181   mCherry cntr1 GSM1272460   source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf mCherry cntr1 Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies. Zebrafish 5 dpf liver   Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends.   genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf GSM1272460 GSM1272460: mCherry cntr1; Danio rerio; RNA Seq GSM1272460   1 Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends. GEO Accession:GSM1272460 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP033231     mCherry_cntr1.fastq.gz fastq 2098395500.0 20983955.0 GSM1272460 r1 0:100 A:533756912;C:521877600;G:512200617;T:528020965;N:2539406 100       533756912 521877600 512200617 528020965 2539406 SRX381136 SRS505528 SRA111986 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.89445   0.02866   0.82426   0.50861   100   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2013-11-21 Larval Larval Liver Liver and Biliary System
37219 37219 SRR1035238 SRX381135 SRS505527 SRP033231 PRJNA229468 Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma GSE52605 Transcriptome Analysis UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish cultured cells and human tumors we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.   pubmed:24486181   UHRF1 hi B GSM1272459   source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf UHRF1 hi B Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies. Zebrafish 5 dpf liver   Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends.   genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf GSM1272459 GSM1272459: UHRF1 hi B; Danio rerio; RNA Seq GSM1272459   1 Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends. GEO Accession:GSM1272459 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP033231     UHRF1_hi_B.fastq.gz fastq 2127061900.0 21270619.0 GSM1272459 r1 0:100 A:540147604;C:542900044;G:522760277;T:518703604;N:2550371 100       540147604 542900044 522760277 518703604 2550371 SRX381135 SRS505527 SRA111986 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.7609   0.0395   0.77788   0.51544   100   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2013-11-21 Larval Larval Liver Liver and Biliary System
37220 37220 SRR1035237 SRX381134 SRS505526 SRP033231 PRJNA229468 Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma GSE52605 Transcriptome Analysis UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish cultured cells and human tumors we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.   pubmed:24486181   UHRF1 hi A GSM1272458   source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf UHRF1 hi A Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies. Zebrafish 5 dpf liver   Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends.   genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf GSM1272458 GSM1272458: UHRF1 hi A; Danio rerio; RNA Seq GSM1272458   1 Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible bar coded adapters were ligated to both ends. GEO Accession:GSM1272458 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP033231     UHRF1_hi_A.fastq.gz fastq 2476218900.0 24762189.0 GSM1272458 r1 0:100 A:625575890;C:631605318;G:620422311;T:595617894;N:2997487 100       625575890 631605318 620422311 595617894 2997487 SRX381134 SRS505526 SRA111986 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.80154   0.04243   0.80409   0.50831   100   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2013-11-21 Larval Larval Liver Liver and Biliary System
37271 37271 SRR1050719 SRX392663 SRS515660 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X+M D+ GSM1289483   source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline X+M D+ The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline GSM1289483 GSM1289483: X+M D+; Danio rerio; RNA Seq GSM1289483   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289483 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X+M-D+.csfasta.gz X+M-D+.qual SOLiD_native SOLiD_native 367532585.0 10500931.0 GSM1289483 r1 0:35 0:113917936;1:90770860;2:74839037;3:87267038;.:737714 35                 SRX392663 SRS515660 SRA117588 GEO National University of Singapore 1 0.03142   0.01041   0.99115   0.47722   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37272 37272 SRR1050718 SRX392662 SRS515661 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X M+D+ GSM1289482   source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline X M+D+ The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline GSM1289482 GSM1289482: X M+D+; Danio rerio; RNA Seq GSM1289482   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289482 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X-M+D+.csfasta.gz X-M+D+.qual SOLiD_native SOLiD_native 524940885.0 14998311.0 GSM1289482 r1 0:35 0:177873348;1:126792787;2:107434769;3:111636161;.:1203820 35                 SRX392662 SRS515661 SRA117588 GEO National University of Singapore 1 0.04433   0.02519   0.99456   0.5443   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37273 37273 SRR1050717 SRX392661 SRS515658 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X M D+ GSM1289481   source name:control liver|tissue:liver|genotype:wildtype sibling|agent:doxycycline X M D+ The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:wildtype sibling|agent:doxycycline GSM1289481 GSM1289481: X M D+; Danio rerio; RNA Seq GSM1289481   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289481 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X-M-D+.csfasta.gz X-M-D+.qual SOLiD_native SOLiD_native 503677265.0 14390779.0 GSM1289481 r1 0:35 0:153190412;1:124381654;2:106372352;3:118615876;.:1116971 35                 SRX392661 SRS515658 SRA117588 GEO National University of Singapore 1 0.03136   0.01201   0.99356   0.49598   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37274 37274 SRR1050716 SRX392660 SRS515659 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X+M D GSM1289480   source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1 X+M D The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1 GSM1289480 GSM1289480: X+M D ; Danio rerio; RNA Seq GSM1289480   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289480 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X+M-D-.csfasta.gz X+M-D-.qual SOLiD_native SOLiD_native 634523960.0 18129256.0 GSM1289480 r1 0:35 0:234010528;1:135057441;2:132344184;3:131577105;.:1534702 35                 SRX392660 SRS515659 SRA117588 GEO National University of Singapore 1 0.06814   0.05142   0.99579   0.6174   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37275 37275 SRR1050715 SRX392659 SRS515657 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X M+D GSM1289479   source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1 X M+D The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1 GSM1289479 GSM1289479: X M+D ; Danio rerio; RNA Seq GSM1289479   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289479 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X-M+D-.csfasta.gz X-M+D-.qual SOLiD_native SOLiD_native 417548565.0 11929959.0 GSM1289479 r1 0:35 0:114209112;1:103552786;2:91302789;3:107590004;.:893874 35                 SRX392659 SRS515657 SRA117588 GEO National University of Singapore 1 0.02253   0.00519   0.99218   0.61466   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37276 37276 SRR1050714 SRX392658 SRS515656 SRP034513 PRJNA231764 Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer GSE53342 Transcriptome Analysis To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D X M+D X M D+ xmrk tumor sample X+M D+ and control samples X M D X+M D X M D+ were generated by deep sequencing using three prime RNA SAGE on SOLiD system   pubmed:24633177   X M D GSM1289478   source name:control liver|tissue:liver|genotype:wildtype sibling|agent:n1 X M D The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype:wildtype sibling|agent:n1 GSM1289478 GSM1289478: X M D ; Danio rerio; RNA Seq GSM1289478   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1289478 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD System 3.0   SRP034513     X-M-D-.csfasta.gz X-M-D-.qual SOLiD_native SOLiD_native 522827305.0 14937923.0 GSM1289478 r1 0:35 0:143962506;1:130748449;2:106995057;3:140038917;.:1082376 35                 SRX392658 SRS515656 SRA117588 GEO National University of Singapore 1 0.02926   0.00817   0.99022   0.53421   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-16 Adult Adult Liver Liver and Biliary System
37277 37277 SRR1057959 SRX398517 SRS518969 SRP034710 PRJNA232516 Transcriptomic analyses of Kras induced zebrafish liver cancer GSE53630 Transcriptome Analysis The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system   pubmed:24633177   6T2 GSM1297515   source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis 6T2 The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis GSM1297515 GSM1297515: 6T2; Danio rerio; RNA Seq GSM1297515   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1297515 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP034710     6T2.csfasta.gz 6T2.qual.gz SOLiD_native SOLiD_native 818910190.0 23397434.0 GSM1297515 r1 0:35 0:347259734;1:164743259;2:162029194;3:130508344;.:14369659 35                 SRX398517 SRS518969 SRA122333 GEO National University of Singapore 1 0.03756   0.0064   0.99931   0.92063   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-24 Undetermined Adult Liver Liver and Biliary System
37278 37278 SRR1057958 SRX398516 SRS518968 SRP034710 PRJNA232516 Transcriptomic analyses of Kras induced zebrafish liver cancer GSE53630 Transcriptome Analysis The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system   pubmed:24633177   6T1 GSM1297514   source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis 6T1 The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. liver tumor one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis GSM1297514 GSM1297514: 6T1; Danio rerio; RNA Seq GSM1297514   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1297514 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP034710     6T1.csfasta.gz 6T1.qual.gz SOLiD_native SOLiD_native 761241005.0 21749743.0 GSM1297514 r1 0:35 0:306840116;1:164725874;2:160786359;3:126370697;.:2517959 35                 SRX398516 SRS518968 SRA122333 GEO National University of Singapore 1 0.0542   0.00664   0.99876   0.95184   35   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-24 Undetermined Adult Liver Liver and Biliary System
37279 37279 SRR1057957 SRX398515 SRS518967 SRP034710 PRJNA232516 Transcriptomic analyses of Kras induced zebrafish liver cancer GSE53630 Transcriptome Analysis The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system   pubmed:24633177   6M2 GSM1297513   source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control 6M2 The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control GSM1297513 GSM1297513: 6M2; Danio rerio; RNA Seq GSM1297513   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1297513 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP034710     6M2.csfasta.gz 6M2.qual.gz SOLiD_native SOLiD_native 627546330.0 20918211.0 GSM1297513 r1 0:30 0:265606277;1:113800100;2:158432886;3:89099865;.:607202 30                 SRX398515 SRS518967 SRA122333 GEO National University of Singapore 1 0.28369   0.05854   0.97611   0.92541   30   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-24 Undetermined Adult Liver Liver and Biliary System
37280 37280 SRR1057956 SRX398514 SRS518966 SRP034710 PRJNA232516 Transcriptomic analyses of Kras induced zebrafish liver cancer GSE53630 Transcriptome Analysis The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing using three prime' RNA SAGE on SOLiD system   pubmed:24633177   6M1 GSM1297512   source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control 6M1 The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM. control liver one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis. Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.   tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control GSM1297512 GSM1297512: 6M1; Danio rerio; RNA Seq GSM1297512   1 Total RNA was extracted using TRIzol Reagent Invitrogen USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol. GEO Accession:GSM1297512 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ABI_SOLID AB SOLiD 3 Plus System   SRP034710     6M1.csfasta.gz 6M1.qual.gz SOLiD_native SOLiD_native 670343910.0 22344797.0 GSM1297512 r1 0:30 0:270812672;1:123662771;2:177982653;3:97335698;.:550116 30                 SRX398514 SRS518966 SRA122333 GEO National University of Singapore 1 0.28477   0.05061   0.9735   0.86701   30   B   usable mapping rate legacy early unknown cdna_unspecified unknown bulk unknown unknown   Singapore 2013-12-24 Undetermined Adult Liver Liver and Biliary System
37985 37985 SRR1216351 SRX510531 SRS588958 SRP040940 PRJNA243510 Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish GSE56498 Transcriptome Analysis ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase FASN. Overall design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. parent bioproject:PRJNA541472 pubmed:24874946   nls Cherry Ethanol #2 GSM1362715   tissue:Zebrafish 5 dpf liver|tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf nls Cherry Ethanol #2 Illumina CASAVA version 1.7 used for basecalling ? Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes reads and their frequencies. Zebrafish 5 dpf liver   Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries.   tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf GSM1362715 GSM1362715: nls Cherry Ethanol #2; Danio rerio; ncRNA Seq GSM1362715   1 Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. GEO Accession:GSM1362715 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP040940     Cherry2-ethanol_raw.txt.gz fastq 2547597500.0 25475975.0 GSM1362715 r1 0:100 A:667878423;C:617022069;G:603019059;T:656604341;N:3073608 100       667878423 617022069 603019059 656604341 3073608 SRX510531 SRS588958 SRA156310 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.903   0.06203   0.78173   0.47105   100   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-04-03 Larval Larval Liver Liver and Biliary System
37986 37986 SRR1216350 SRX510530 SRS588959 SRP040940 PRJNA243510 Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish GSE56498 Transcriptome Analysis ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase FASN. Overall design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. parent bioproject:PRJNA541472 pubmed:24874946   nls Cherry Ethanol #1 GSM1362714   tissue:Zebrafish 5 dpf liver|tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf nls Cherry Ethanol #1 Illumina CASAVA version 1.7 used for basecalling ? Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes reads and their frequencies. Zebrafish 5 dpf liver   Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries.   tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf GSM1362714 GSM1362714: nls Cherry Ethanol #1; Danio rerio; ncRNA Seq GSM1362714   1 Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. GEO Accession:GSM1362714 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP040940     Cherry1-ethanol_raw.txt.gz fastq 2848772300.0 28487723.0 GSM1362714 r1 0:100 A:754173668;C:673034180;G:669171787;T:748900638;N:3492027 100       754173668 673034180 669171787 748900638 3492027 SRX510530 SRS588959 SRA156310 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.93424   0.04344   0.80365   0.45184   100   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-04-03 Larval Larval Liver Liver and Biliary System
37987 37987 SRR1216349 SRX510529 SRS588957 SRP040940 PRJNA243510 Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish GSE56498 Transcriptome Analysis ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase FASN. Overall design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. parent bioproject:PRJNA541472 pubmed:24874946   nAtf6 Cherry #1 GSM1362713   tissue:Zebrafish 5 dpf liver|tissue type:liver|genotype:Tgfabp10:nAtf6 cherry; cmlc2:GFP|developmental stage:5 dpf nAtf6 Cherry #1 Illumina CASAVA version 1.7 used for basecalling ? Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes reads and their frequencies. Zebrafish 5 dpf liver   Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries.   tissue type:liver|genotype:Tgfabp10:nAtf6 cherry; cmlc2:GFP|developmental stage:5 dpf GSM1362713 GSM1362713: nAtf6 Cherry #1; Danio rerio; ncRNA Seq GSM1362713   1 Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. GEO Accession:GSM1362713 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP040940     nAtf61_raw.txt.gz fastq 2259581400.0 22595814.0 GSM1362713 r1 0:100 A:577752854;C:550694305;G:551105918;T:577235877;N:2792446 100       577752854 550694305 551105918 577235877 2792446 SRX510529 SRS588957 SRA156310 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.94581   0.04947   0.80375   0.52352   100   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-04-03 Larval Larval Liver Liver and Biliary System
37988 37988 SRR1216348 SRX510528 SRS588956 SRP040940 PRJNA243510 Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish GSE56498 Transcriptome Analysis ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase FASN. Overall design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. parent bioproject:PRJNA541472 pubmed:24874946   nls Cherry #2 GSM1362712   tissue:Zebrafish 5 dpf liver|tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf nls Cherry #2 Illumina CASAVA version 1.7 used for basecalling ? Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes reads and their frequencies. Zebrafish 5 dpf liver   Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries.   tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf GSM1362712 GSM1362712: nls Cherry #2; Danio rerio; ncRNA Seq GSM1362712   1 Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. GEO Accession:GSM1362712 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP040940     Cherry2_raw.txt.gz fastq 2132003100.0 21320031.0 GSM1362712 r1 0:100 A:536532013;C:533562250;G:522685362;T:536641910;N:2581565 100       536532013 533562250 522685362 536641910 2581565 SRX510528 SRS588956 SRA156310 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.88352   0.04379   0.81947   0.52367   100   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-04-03 Larval Larval Liver Liver and Biliary System
37989 37989 SRR1216347 SRX510527 SRS588955 SRP040940 PRJNA243510 Activating transcription factor 6 is necessary and sufficient for alcoholic fatty liver disease in zebrafish GSE56498 Transcriptome Analysis ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase FASN. Overall design: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. parent bioproject:PRJNA541472 pubmed:24874946   nls Cherry #1 GSM1362711   tissue:Zebrafish 5 dpf liver|tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf nls Cherry #1 Illumina CASAVA version 1.7 used for basecalling ? Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al. 2008; Olson et al. 2008; Tam et al. 2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes reads and their frequencies. Zebrafish 5 dpf liver   Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries.   tissue type:liver|genotype:Tgfabp10:nls mCherry|developmental stage:5 dpf GSM1362711 GSM1362711: nls Cherry #1; Danio rerio; ncRNA Seq GSM1362711   1 Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tgfabp10:nls mCherry control larvae 2 batches of ethanol treated Tgfabp10:nls mCherry larvae and 1 batch of Tgfabp10:nAtf6 cherry; cmlc2:GFP. Each batch was purified for preparation of high throughput sequencing libraries. GEO Accession:GSM1362711 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP040940     Cherry1_raw.txt.gz fastq 2098395500.0 20983955.0 GSM1362711 r1 0:100 A:533756912;C:521877600;G:512200617;T:528020965;N:2539406 100       533756912 521877600 512200617 528020965 2539406 SRX510527 SRS588955 SRA156310 GEO sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai 1 0.89447   0.02865   0.82436   0.50802   100   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2014-04-03 Larval Larval Liver Liver and Biliary System
38003 38003 SRR1265754 SRX529148 SRS598845 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Liver Replicate 3 sRNAseq GSM1376637   source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain Female Liver Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Liver|genetic background:Wild type Singapore strain GSM1376637 GSM1376637: Female Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376637   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376637 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL012_GCCAAT_L008_R1.fastq.gz fastq 105717543.0 2072893.0 GSM1376637 r1 0:51 A:22408978;C:25732405;G:31681641;T:25880225;N:14294 51       22408978 25732405 31681641 25880225 14294 SRX529148 SRS598845 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.05572   0.0017   0.99691   0.56539   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38004 38004 SRR1265753 SRX529147 SRS598844 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Liver Replicate 2 sRNAseq GSM1376636   source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain Female Liver Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Liver|genetic background:Wild type Singapore strain GSM1376636 GSM1376636: Female Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376636   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376636 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL011_ACAGTG_L008_R1.fastq.gz fastq 484614546.0 9502246.0 GSM1376636 r1 0:51 A:98373224;C:113894197;G:148444486;T:123841427;N:61212 51       98373224 113894197 148444486 123841427 61212 SRX529147 SRS598844 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01517   0.00112   0.9964   0.61558   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38005 38005 SRR1265752 SRX529146 SRS598843 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Female Liver Replicate 1 sRNAseq GSM1376635   source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type Singapore strain Female Liver Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Female Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Female|tissue:Liver|genetic background:Wild type Singapore strain GSM1376635 GSM1376635: Female Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376635   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376635 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL010_TGACCA_L008_R1.fastq.gz fastq 304949706.0 5979406.0 GSM1376635 r1 0:51 A:62732698;C:71083849;G:92267430;T:78825237;N:40492 51       62732698 71083849 92267430 78825237 40492 SRX529146 SRS598843 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.01218   0.001   0.99709   0.55264   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38006 38006 SRR1265751 SRX529145 SRS598842 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Liver Replicate 3 sRNAseq GSM1376634   source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain Male Liver Replicate 3 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Liver|genetic background:Wild type Singapore strain GSM1376634 GSM1376634: Male Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq GSM1376634   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376634 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL009_GATCAG_L007_R1.fastq.gz fastq 287383266.0 5634966.0 GSM1376634 r1 0:51 A:54829818;C:73200212;G:89994996;T:69332773;N:25467 51       54829818 73200212 89994996 69332773 25467 SRX529145 SRS598842 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00273   0.00026   0.99791   0.69537   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38007 38007 SRR1265750 SRX529144 SRS598841 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Liver Replicate 2 sRNAseq GSM1376633   source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain Male Liver Replicate 2 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Liver|genetic background:Wild type Singapore strain GSM1376633 GSM1376633: Male Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq GSM1376633   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376633 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL008_ACTTGA_L007_R1.fastq.gz fastq 595761753.0 11681603.0 GSM1376633 r1 0:51 A:111507488;C:155297338;G:186229891;T:142672923;N:54113 51       111507488 155297338 186229891 142672923 54113 SRX529144 SRS598841 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00597   0.00067   0.99679   0.72807   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38008 38008 SRR1265749 SRX529143 SRS598840 SRP041544 PRJNA245824 Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish GSE57169 Transcriptome Analysis The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.   pubmed:26574018   Male Liver Replicate 1 sRNAseq GSM1376632   source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type Singapore strain Male Liver Replicate 1 sRNAseq Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. Male Liver N/A Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. Fishes were purchased from a local supplier and acclimatized before tissue extraction. gender:Male|tissue:Liver|genetic background:Wild type Singapore strain GSM1376632 GSM1376632: Male Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq GSM1376632   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. GEO Accession:GSM1376632 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP041544     MZL007_CAGATC_L007_R1.fastq.gz fastq 976402599.0 19145149.0 GSM1376632 r1                       SRX529143 SRS598840 SRA160430 GEO Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore 1 0.00348   0.00035   0.99742   0.69292   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Liver Liver and Biliary System
38289 38289 SRR1731761 SRX828260 SRS807370 SRP051449 PRJNA266270 Danio rerio Transcriptome or Gene expression PRJNA266270 Other To identify molecular signals that initiate liver regeneration post 1/3 PH         sham operated liver transcriptome post 1/3 PH   breed:AB line|cultivar:AB line|strain:AB line|age:10 month|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 sham operated liver transcriptome post 1/3 PH sham operated 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP051449     sham-operated_R1.fastq.gz sham-operated_R2.fastq.gz fastq fastq 2339904960.0 16249340.0 sham operated 0:72 1:72 A:639730953;C:549099184;G:603489762;T:545135156;N:2449905 72 72     639730953 549099184 603489762 545135156 2449905 SRX828260 SRS807370 SRA223828 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.9353 0.91074 0.02617 0.0253 0.86334 0.86387 0.35902 0.36066 72 72 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2016-02-05 Adult Adult Liver Liver and Biliary System
38290 38290 SRR1731762 SRX821156 SRS800969 SRP051449 PRJNA266270 Danio rerio Transcriptome or Gene expression PRJNA266270 Other To identify molecular signals that initiate liver regeneration post 1/3 PH         Transcriptome during early stage of liver regeneration post 1/3 PH   breed:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/3 partial hepatectomy D.rereios liver regeneration sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP051449     6h_run1_R1.fastq.gz 6h_run1_R2.fastq.gz fastq fastq 2014108128.0 13986862.0 6h 0:72 1:72 A:542840697;C:473739345;G:521450086;T:473979205;N:2098795 72 72     542840697 473739345 521450086 473979205 2098795 SRX821156 SRS800969 SRA220726 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.92698 0.90124 0.02898 0.0276 0.85141 0.85064 0.41793 0.40779 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
38291 38291 SRR1735290 SRX824451 SRS804070 SRP051556 PRJNA266272 Danio rerio Transcriptome or Gene expression PRJNA266272 Other To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH         transcriptome during liver regeneration post 1/9 PH   breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy D.rerios liver regeneration post 1/9 PH sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP051556     24h3_R1.fastq.gz 24h3_R2.fastq.gz fastq fastq 1569651120.0 10900355.0 24h3 0:72 1:72 A:423126744;C:367185056;G:396200408;T:381254240;N:1884672 72 72     423126744 367185056 396200408 381254240 1884672 SRX824451 SRS804070 SRA221177 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.93264 0.91624 0.03854 0.0375 0.81708 0.81554 0.43719 0.43414 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
38292 38292 SRR1735297 SRX824451 SRS804070 SRP051556 PRJNA266272 Danio rerio Transcriptome or Gene expression PRJNA266272 Other To investigate the mechanism of gene expression profiles and the post transcriptional regulations during liver regeneration post 1/9 PH         transcriptome during liver regeneration post 1/9 PH   breed:AB line|strain:AB line|age:10 month|biomaterial provider:The Key Laboratory of Aquatic Biodiversity and Conservation|sex:female|tissue:liver|BioSampleModel:Model organism or animal                 Transcriptomic characterization of zebrafish liver regeneration post 1/9 partial hepatectomy D.rerios liver regeneration post 1/9 PH sequencing project 1 1     RNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP051556     168h1_R1.fastq.gz 168h1_R2.fastq.gz fastq fastq 2340104400.0 16250725.0 168h1 0:72 1:72 A:667910990;C:526343343;G:603352668;T:540093539;N:2403860 72 72     667910990 526343343 603352668 540093539 2403860 SRX824451 SRS804070 SRA221177 Institute of Hydrobiology, Chinese Academy of Scie|The Key Laboratory of Aquatic Biodiversity and Con Chinese Academy of Sciences 2 0.9275 0.90676 0.03565 0.03486 0.85456 0.85421 0.42251 0.42133 72 72 B B biological fallback assumption illumina early_illumina unknown random_priming unknown bulk unknown unknown   China 2016-02-10 Adult Adult Liver Liver and Biliary System
38413 38413 SRR1821826 SRX893427 SRS859540 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver208 36m 3.75nM roten1 8w rep6 GSM1620973   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver208 36m 3.75nM roten1 8w rep6 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620973 GSM1620973: liver208 36m 3.75nM roten1 8w rep6; Danio rerio; RNA Seq GSM1620973   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620973 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver208.fastq.gz fastq 2200239850.0 44004797.0 GSM1620973 r1 0:50 A:571878023;C:528294946;G:516878213;T:582511055;N:677613 50       571878023 528294946 516878213 582511055 677613 SRX893427 SRS859540 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93543   0.05381   0.814   0.56377   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38414 38414 SRR1821825 SRX893426 SRS859542 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver207 36m 3.75nM roten1 8w rep5 GSM1620972   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver207 36m 3.75nM roten1 8w rep5 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620972 GSM1620972: liver207 36m 3.75nM roten1 8w rep5; Danio rerio; RNA Seq GSM1620972   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620972 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver207.fastq.gz fastq 2434066300.0 48681326.0 GSM1620972 r1 0:50 A:647470716;C:574345677;G:559996925;T:651504881;N:748101 50       647470716 574345677 559996925 651504881 748101 SRX893426 SRS859542 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93196   0.06713   0.79916   0.56304   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38415 38415 SRR1821824 SRX893425 SRS859544 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver206 36m 3.75nM roten1 8w rep4 GSM1620971   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver206 36m 3.75nM roten1 8w rep4 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620971 GSM1620971: liver206 36m 3.75nM roten1 8w rep4; Danio rerio; RNA Seq GSM1620971   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620971 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver206.fastq.gz fastq 2530671200.0 50613424.0 GSM1620971 r1 0:50 A:672377930;C:592838124;G:582426421;T:681213921;N:1814804 50       672377930 592838124 582426421 681213921 1814804 SRX893425 SRS859544 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93349   0.0724   0.7867   0.56433   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38416 38416 SRR1821823 SRX893424 SRS859541 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver205 36m 3.75nM roten1 8w rep3 GSM1620970   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver205 36m 3.75nM roten1 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620970 GSM1620970: liver205 36m 3.75nM roten1 8w rep3; Danio rerio; RNA Seq GSM1620970   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620970 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver205.fastq.gz fastq 2149930050.0 42998601.0 GSM1620970 r1 0:50 A:568725900;C:507812500;G:497024054;T:576280556;N:87040 50       568725900 507812500 497024054 576280556 87040 SRX893424 SRS859541 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93606   0.06193   0.80012   0.57505   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38417 38417 SRR1821822 SRX893423 SRS859543 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver204 36m 3.75nM roten1 8w rep2 GSM1620969   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver204 36m 3.75nM roten1 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620969 GSM1620969: liver204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq GSM1620969   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620969 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver204.fastq.gz fastq 2852874500.0 57057490.0 GSM1620969 r1 0:50 A:758952474;C:670213462;G:651059038;T:770418307;N:2231219 50       758952474 670213462 651059038 770418307 2231219 SRX893423 SRS859543 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92602   0.0709   0.78319   0.55468   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38418 38418 SRR1821821 SRX893422 SRS859545 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver203 36m 3.75nM roten1 8w rep1 GSM1620968   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks liver203 36m 3.75nM roten1 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks GSM1620968 GSM1620968: liver203 36m 3.75nM roten1 8w rep1; Danio rerio; RNA Seq GSM1620968   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620968 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver203.fastq.gz fastq 2686262550.0 53725251.0 GSM1620968 r1 0:50 A:705831052;C:629469709;G:620794974;T:716919571;N:13247244 50       705831052 629469709 620794974 716919571 13247244 SRX893422 SRS859545 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91348   0.05511   0.81347   0.53272   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38419 38419 SRR1821820 SRX893421 SRS859546 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver172 36m 3.75nM roten1 3w rep4 GSM1620967   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks liver172 36m 3.75nM roten1 3w rep4 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620967 GSM1620967: liver172 36m 3.75nM roten1 3w rep4; Danio rerio; RNA Seq GSM1620967   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620967 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver172.fastq.gz fastq 2065136400.0 41302728.0 GSM1620967 r1 0:50 A:547988869;C:486083531;G:472243345;T:557154482;N:1666173 50       547988869 486083531 472243345 557154482 1666173 SRX893421 SRS859546 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92759   0.0626   0.79326   0.52584   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38420 38420 SRR1821819 SRX893420 SRS859547 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver171 36m 3.75nM roten1 3w rep3 GSM1620966   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks liver171 36m 3.75nM roten1 3w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620966 GSM1620966: liver171 36m 3.75nM roten1 3w rep3; Danio rerio; RNA Seq GSM1620966   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620966 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver171.fastq.gz fastq 2410165800.0 48203316.0 GSM1620966 r1 0:50 A:638532163;C:560800416;G:550477924;T:648424639;N:11930658 50       638532163 560800416 550477924 648424639 11930658 SRX893420 SRS859547 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9052   0.07216   0.77013   0.54156   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38421 38421 SRR1821818 SRX893419 SRS859548 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver170 36m 3.75nM roten1 3w rep2 GSM1620965   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks liver170 36m 3.75nM roten1 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620965 GSM1620965: liver170 36m 3.75nM roten1 3w rep2; Danio rerio; RNA Seq GSM1620965   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620965 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver170.fastq.gz fastq 2077713200.0 41554264.0 GSM1620965 r1 0:50 A:547665152;C:493031219;G:478885586;T:558030382;N:100861 50       547665152 493031219 478885586 558030382 100861 SRX893419 SRS859548 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92951   0.06604   0.78813   0.50562   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38422 38422 SRR1821817 SRX893418 SRS859549 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver168 36m 3.75nM roten1 3w rep1 GSM1620964   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks liver168 36m 3.75nM roten1 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks GSM1620964 GSM1620964: liver168 36m 3.75nM roten1 3w rep1; Danio rerio; RNA Seq GSM1620964   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620964 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver168.fastq.gz fastq 2043972800.0 40879456.0 GSM1620964 r1 0:50 A:537874539;C:485494677;G:472924858;T:547619633;N:59093 50       537874539 485494677 472924858 547619633 59093 SRX893418 SRS859549 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93165   0.06093   0.78443   0.51626   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38423 38423 SRR1821816 SRX893417 SRS859550 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver188 36m control 8w rep3 GSM1620963   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks liver188 36m control 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:n1|duration:8 weeks GSM1620963 GSM1620963: liver188 36m control 8w rep3; Danio rerio; RNA Seq GSM1620963   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620963 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver188.fastq.gz fastq 2043860700.0 40877214.0 GSM1620963 r1 0:50 A:546509644;C:480578060;G:467994052;T:548137833;N:641111 50       546509644 480578060 467994052 548137833 641111 SRX893417 SRS859550 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91484   0.08158   0.7559   0.57112   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38424 38424 SRR1821815 SRX893416 SRS859551 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver186 36m control 8w rep2 GSM1620962   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks liver186 36m control 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:n1|duration:8 weeks GSM1620962 GSM1620962: liver186 36m control 8w rep2; Danio rerio; RNA Seq GSM1620962   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620962 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver186.fastq.gz fastq 1806504400.0 36130088.0 GSM1620962 r1 0:50 A:478503997;C:426614556;G:417975841;T:482136404;N:1273602 50       478503997 426614556 417975841 482136404 1273602 SRX893416 SRS859551 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93167   0.06499   0.79695   0.53466   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38425 38425 SRR1821814 SRX893415 SRS859552 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver185 36m control 8w rep1 GSM1620961   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks liver185 36m control 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:n1|duration:8 weeks GSM1620961 GSM1620961: liver185 36m control 8w rep1; Danio rerio; RNA Seq GSM1620961   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620961 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver185.fastq.gz fastq 2656526050.0 53130521.0 GSM1620961 r1 0:50 A:700055044;C:626738929;G:622660107;T:706999824;N:72146 50       700055044 626738929 622660107 706999824 72146 SRX893415 SRS859552 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92972   0.05926   0.8001   0.55293   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38426 38426 SRR1821813 SRX893414 SRS859555 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver162 36m control 3w rep2 GSM1620960   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:3 weeks liver162 36m control 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:n1|duration:3 weeks GSM1620960 GSM1620960: liver162 36m control 3w rep2; Danio rerio; RNA Seq GSM1620960   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620960 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver162.fastq.gz fastq 2037943300.0 40758866.0 GSM1620960 r1 0:50 A:532287036;C:487343893;G:476293186;T:541912735;N:106450 50       532287036 487343893 476293186 541912735 106450 SRX893414 SRS859555 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92256   0.05731   0.79582   0.52548   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38427 38427 SRR1821812 SRX893413 SRS859553 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver161 36m control 3w rep1 GSM1620959   source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:3 weeks liver161 36m control 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:36 month|treatment:n1|duration:3 weeks GSM1620959 GSM1620959: liver161 36m control 3w rep1; Danio rerio; RNA Seq GSM1620959   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620959 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver161.fastq.gz fastq 1931855350.0 38637107.0 GSM1620959 r1 0:50 A:506162541;C:457810984;G:450391101;T:513259108;N:4231616 50       506162541 457810984 450391101 513259108 4231616 SRX893413 SRS859553 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91267   0.06115   0.78224   0.54531   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38428 38428 SRR1821811 SRX893412 SRS859554 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver184 12m control 8w rep3 GSM1620958   source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks liver184 12m control 8w rep3 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:12 month|treatment:n1|duration:8 weeks GSM1620958 GSM1620958: liver184 12m control 8w rep3; Danio rerio; RNA Seq GSM1620958   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620958 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver184.fastq.gz fastq 2612886200.0 52257724.0 GSM1620958 r1 0:50 A:692472911;C:614541298;G:602942228;T:702823776;N:105987 50       692472911 614541298 602942228 702823776 105987 SRX893412 SRS859554 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93487   0.06068   0.81237   0.58828   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38429 38429 SRR1821810 SRX893411 SRS859556 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver183 12m control 8w rep2 GSM1620957   source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks liver183 12m control 8w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:12 month|treatment:n1|duration:8 weeks GSM1620957 GSM1620957: liver183 12m control 8w rep2; Danio rerio; RNA Seq GSM1620957   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620957 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver183.fastq.gz fastq 3008273200.0 60165464.0 GSM1620957 r1 0:50 A:805204411;C:700890541;G:683878902;T:816000323;N:2299023 50       805204411 700890541 683878902 816000323 2299023 SRX893411 SRS859556 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9234   0.07513   0.79884   0.50199   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38430 38430 SRR1821809 SRX893410 SRS859559 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver182 12m control 8w rep1 GSM1620956   source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks liver182 12m control 8w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:12 month|treatment:n1|duration:8 weeks GSM1620956 GSM1620956: liver182 12m control 8w rep1; Danio rerio; RNA Seq GSM1620956   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620956 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver182.fastq.gz fastq 2315532750.0 46310655.0 GSM1620956 r1 0:50 A:614278228;C:536988118;G:528915286;T:623991113;N:11360005 50       614278228 536988118 528915286 623991113 11360005 SRX893410 SRS859559 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.91729   0.06968   0.79778   0.57634   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38431 38431 SRR1821808 SRX893409 SRS859557 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver159 12m control 3w rep2 GSM1620955   source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:3 weeks liver159 12m control 3w rep2 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:12 month|treatment:n1|duration:3 weeks GSM1620955 GSM1620955: liver159 12m control 3w rep2; Danio rerio; RNA Seq GSM1620955   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620955 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver159.fastq.gz fastq 1787795950.0 35755919.0 GSM1620955 r1 0:50 A:475365731;C:420351773;G:409097689;T:482893599;N:87158 50       475365731 420351773 409097689 482893599 87158 SRX893409 SRS859557 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92805   0.07018   0.7839   0.57353   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
38432 38432 SRR1821807 SRX893408 SRS859558 SRP055573 PRJNA276667 RNA seq of zebrafish brain liver and skin during perturbation with rotenone at young and old age GSE66362 Transcriptome Analysis Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain liver skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group   pubmed:27135165   liver157 12m control 3w rep1 GSM1620954   source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:3 weeks liver157 12m control 3w rep1 FASTQ files were extracted using Illumina Casava software v1.8.2. total RNA extracted from liver Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and 8 weeks respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks. Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. Zebrafish Danio rerio were raised under standard conditions. tissue:liver|age:12 month|treatment:n1|duration:3 weeks GSM1620954 GSM1620954: liver157 12m control 3w rep1; Danio rerio; RNA Seq GSM1620954   1 Total RNA was isolated using QIAzol Qiagen Hilden Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab Erlangen Germany and stored at 80 °C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA USA following the manufacturer's instruction. GEO Accession:GSM1620954 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP055573     Liver157.fastq.gz fastq 2375584950.0 47511699.0 GSM1620954 r1 0:50 A:636438966;C:553591776;G:539104775;T:646382105;N:67328 50       636438966 553591776 539104775 646382105 67328 SRX893408 SRS859558 SRA244883 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.92658   0.07029   0.76359   0.50995   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Germany 2015-02-27 Adult Adult Liver Liver and Biliary System
39999 39999 SRR6081857 SRX3220844 SRS2545507 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 93+94 GSM2795185   source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver NH FLI liver 93+94 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from skin   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver GSM2795185 GSM2795185: NH FLI liver 93+94; Danio rerio; RNA Seq GSM2795185   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM2795185 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_6m_DR93DR94.fq.gz fastq 2333496400.0 46669928.0 GSM2795185 r1 0:50 A:614203790;C:555535741;G:543915663;T:619744641;N:96565 50       614203790 555535741 543915663 619744641 96565 SRX3220844 SRS2545507 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94566   0.08285   0.68876   0.54555   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-09-27 Adult Adult Liver Liver and Biliary System
40000 40000 SRR6081856 SRX3220843 SRS2545506 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI skin 124 GSM2795184   source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:12 month|age category: |tissue:liver NH FLI skin 124 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from skin   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:12 month|age category: |tissue:liver GSM2795184 GSM2795184: NH FLI skin 124; Danio rerio; RNA Seq GSM2795184   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM2795184 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_12m_DR124.fq.gz fastq 2804419350.0 56088387.0 GSM2795184 r1 0:50 A:727789828;C:665886619;G:674182975;T:736335760;N:224168 50       727789828 665886619 674182975 736335760 224168 SRX3220843 SRS2545506 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96193   0.04063   0.7895   0.23278   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-09-27 Adult Adult Liver Liver and Biliary System
40026 40026 SRR2751019 SRX1362089 SRS1125438 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 112 GSM1915525   source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver NH FLI liver 112 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver GSM1915525 GSM1915525: NH FLI liver 112; Danio rerio; RNA Seq GSM1915525   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915525 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_42m_DR112.fq.gz fastq 2493027200.0 49860544.0 GSM1915525 r1 0:50 A:655270619;C:590132953;G:584855596;T:662626178;N:141854 50       655270619 590132953 584855596 662626178 141854 SRX1362089 SRS1125438 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94015   0.06186   0.80777   0.56276   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40027 40027 SRR2751018 SRX1362088 SRS1125437 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 110 GSM1915524   source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver NH FLI liver 110 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver GSM1915524 GSM1915524: NH FLI liver 110; Danio rerio; RNA Seq GSM1915524   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915524 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_42m_DR110.fq.gz fastq 2548926150.0 50978523.0 GSM1915524 r1 0:50 A:664677096;C:610795768;G:599120861;T:674104114;N:228311 50       664677096 610795768 599120861 674104114 228311 SRX1362088 SRS1125437 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9507   0.06053   0.8127   0.51968   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40028 40028 SRR2751017 SRX1362087 SRS1125440 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 109 GSM1915523   source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver NH FLI liver 109 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver GSM1915523 GSM1915523: NH FLI liver 109; Danio rerio; RNA Seq GSM1915523   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915523 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_42m_DR109.fq.gz fastq 2349260700.0 46985214.0 GSM1915523 r1 0:50 A:619110926;C:556823390;G:547569893;T:625605583;N:150908 50       619110926 556823390 547569893 625605583 150908 SRX1362087 SRS1125440 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94144   0.06318   0.76282   0.57815   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40029 40029 SRR2751016 SRX1362086 SRS1125439 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 107 GSM1915522   source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver NH FLI liver 107 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver GSM1915522 GSM1915522: NH FLI liver 107; Danio rerio; RNA Seq GSM1915522   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915522 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_42m_DR107.fq.gz fastq 2819134200.0 56382684.0 GSM1915522 r1 0:50 A:739388911;C:669956842;G:658589434;T:750229539;N:969474 50       739388911 669956842 658589434 750229539 969474 SRX1362086 SRS1125439 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94944   0.06329   0.79433   0.5582   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40030 40030 SRR2751015 SRX1362085 SRS1125441 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 106 GSM1915521   source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver NH FLI liver 106 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver GSM1915521 GSM1915521: NH FLI liver 106; Danio rerio; RNA Seq GSM1915521   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915521 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_42m_DR106.fq.gz fastq 2607094700.0 52141894.0 GSM1915521 r1 0:50 A:684681493;C:617936279;G:611124933;T:692780900;N:571095 50       684681493 617936279 611124933 692780900 571095 SRX1362085 SRS1125441 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94017   0.06883   0.77187   0.53057   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40031 40031 SRR2751014 SRX1362084 SRS1125443 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 152 GSM1915520   source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver NH FLI liver 152 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver GSM1915520 GSM1915520: NH FLI liver 152; Danio rerio; RNA Seq GSM1915520   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915520 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_36m_DR152.fq.gz fastq 3427372500.0 68547450.0 GSM1915520 r1 0:50 A:878643380;C:836548343;G:816844380;T:894177988;N:1158409 50       878643380 836548343 816844380 894177988 1158409 SRX1362084 SRS1125443 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94444   0.06122   0.77875   0.56481   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40032 40032 SRR2751013 SRX1362083 SRS1125442 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 151 GSM1915519   source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver NH FLI liver 151 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver GSM1915519 GSM1915519: NH FLI liver 151; Danio rerio; RNA Seq GSM1915519   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915519 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_36m_DR151.fq.gz fastq 2485583750.0 49711675.0 GSM1915519 r1 0:50 A:660843418;C:585986685;G:573818543;T:664714547;N:220557 50       660843418 585986685 573818543 664714547 220557 SRX1362083 SRS1125442 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93011   0.08086   0.7695   0.5595   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40033 40033 SRR2751012 SRX1362082 SRS1125444 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 150 GSM1915518   source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver NH FLI liver 150 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver GSM1915518 GSM1915518: NH FLI liver 150; Danio rerio; RNA Seq GSM1915518   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915518 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_36m_DR150.fq.gz fastq 2519190600.0 50383812.0 GSM1915518 r1 0:50 A:655881049;C:600722119;G:600690081;T:661791601;N:105750 50       655881049 600722119 600690081 661791601 105750 SRX1362082 SRS1125444 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94575   0.05521   0.82333   0.58307   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40034 40034 SRR2751011 SRX1362081 SRS1125446 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 147 GSM1915517   source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver NH FLI liver 147 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver GSM1915517 GSM1915517: NH FLI liver 147; Danio rerio; RNA Seq GSM1915517   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915517 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_36m_DR147.fq.gz fastq 2259586100.0 45191722.0 GSM1915517 r1 0:50 A:598439339;C:531150489;G:524393660;T:605396290;N:206322 50       598439339 531150489 524393660 605396290 206322 SRX1362081 SRS1125446 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93951   0.05741   0.82063   0.5414   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40035 40035 SRR2751010 SRX1362080 SRS1125413 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 146 GSM1915516   source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver NH FLI liver 146 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver GSM1915516 GSM1915516: NH FLI liver 146; Danio rerio; RNA Seq GSM1915516   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915516 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_36m_DR146.fq.gz fastq 2286592350.0 45731847.0 GSM1915516 r1 0:50 A:575985495;C:563341201;G:554727838;T:592210592;N:327224 50       575985495 563341201 554727838 592210592 327224 SRX1362080 SRS1125413 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94558   0.05047   0.7904   0.56079   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40036 40036 SRR2751009 SRX1362079 SRS1125409 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 138 GSM1915515   source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver NH FLI liver 138 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu|age:24 month|age category: |tissue:liver GSM1915515 GSM1915515: NH FLI liver 138; Danio rerio; RNA Seq GSM1915515   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915515 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_24m_DR138.fq.gz fastq 3843216450.0 76864329.0 GSM1915515 r1 0:50 A:1018176854;C:908623218;G:891363243;T:1024377821;N:675314 50       1018176854 908623218 891363243 1024377821 675314 SRX1362079 SRS1125409 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9442   0.06874   0.76264   0.52537   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40037 40037 SRR2751008 SRX1362078 SRS1125408 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 136 GSM1915514   source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver NH FLI liver 136 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu|age:24 month|age category: |tissue:liver GSM1915514 GSM1915514: NH FLI liver 136; Danio rerio; RNA Seq GSM1915514   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915514 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_24m_DR136.fq.gz fastq 3668583250.0 73371665.0 GSM1915514 r1 0:50 A:961648869;C:879998251;G:866556900;T:960048700;N:330530 50       961648869 879998251 866556900 960048700 330530 SRX1362078 SRS1125408 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93746   0.06166   0.80389   0.52831   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40038 40038 SRR2751007 SRX1362077 SRS1125445 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 135 GSM1915513   source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver NH FLI liver 135 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu|age:24 month|age category: |tissue:liver GSM1915513 GSM1915513: NH FLI liver 135; Danio rerio; RNA Seq GSM1915513   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915513 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_24m_DR135.fq.gz fastq 2511261600.0 50225232.0 GSM1915513 r1 0:50 A:668637105;C:587542062;G:579925851;T:674944365;N:212217 50       668637105 587542062 579925851 674944365 212217 SRX1362077 SRS1125445 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9436   0.09452   0.76958   0.54588   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40039 40039 SRR2751006 SRX1362076 SRS1125447 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 134 GSM1915512   source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver NH FLI liver 134 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu|age:24 month|age category: |tissue:liver GSM1915512 GSM1915512: NH FLI liver 134; Danio rerio; RNA Seq GSM1915512   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915512 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_24m_DR134.fq.gz fastq 2496794600.0 49935892.0 GSM1915512 r1 0:50 A:657127337;C:591970066;G:582273775;T:664995064;N:428358 50       657127337 591970066 582273775 664995064 428358 SRX1362076 SRS1125447 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94435   0.06912   0.78354   0.54526   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40040 40040 SRR2751005 SRX1362075 SRS1125410 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 133 GSM1915511   source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver NH FLI liver 133 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu|age:24 month|age category: |tissue:liver GSM1915511 GSM1915511: NH FLI liver 133; Danio rerio; RNA Seq GSM1915511   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915511 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_24m_DR133.fq.gz fastq 2364294900.0 47285898.0 GSM1915511 r1 0:50 A:621349333;C:562020902;G:553860502;T:626647310;N:416853 50       621349333 562020902 553860502 626647310 416853 SRX1362075 SRS1125410 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94368   0.07791   0.73198   0.53494   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40041 40041 SRR2751004 SRX1362074 SRS1125448 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 126 GSM1915510   source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver NH FLI liver 126 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver GSM1915510 GSM1915510: NH FLI liver 126; Danio rerio; RNA Seq GSM1915510   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915510 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_12m_DR126.fq.gz fastq 2614833700.0 52296674.0 GSM1915510 r1 0:50 A:676534455;C:632762889;G:618276106;T:686974287;N:285963 50       676534455 632762889 618276106 686974287 285963 SRX1362074 SRS1125448 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95004   0.04888   0.82544   0.56527   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System
40042 40042 SRR2751003 SRX1362073 SRS1125449 SRP065208 PRJNA299585 Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain liver skin GSE74244 Transcriptome Analysis Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6 12 24 36 42 month; 3 tissues brain liver skin; 5 samples per group   pubmed:29382830   NH FLI liver 125 GSM1915509   source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver NH FLI liver 125 Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account: tophat2 p 24 o OUTPUTDIR g 1 no coverage search transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count quiet stranded=no idattr=gene id mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample total RNA extracted from liver   Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction.   strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver GSM1915509 GSM1915509: NH FLI liver 125; Danio rerio; RNA Seq GSM1915509   1 Total RNA from was extracted as described Baumgart et al. 2012; PMID:22487494 Preparation of libraries was done using Illumina’s TruSeq RNA sample prep kit following the manufacturer’s instruction. GEO Accession:GSM1915509 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP065208     liver_12m_DR125.fq.gz fastq 2263792150.0 45275843.0 GSM1915509 r1 0:50 A:595799795;C:537810224;G:528914425;T:601165834;N:101872 50       595799795 537810224 528914425 601165834 101872 SRX1362073 SRS1125449 SRA306458 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94421   0.06353   0.79028   0.57064   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2015-10-21 Adult Adult Liver Liver and Biliary System

Next page

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;