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,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,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,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,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,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
28496,SRR26321412,SRX22029502,SRS19102283,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 1,R27,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R27,R27,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R27.fastq,fastq,23400.0,312.0,R27.fastq,0:75,A:7949;C:4612;G:4730;T:6100;N:9,75,,,,7949,4612,4730,6100,9,SRX22029502,SRS19102283,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89642,,0.06772,,0.99827,,0.75,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28497,SRR26321413,SRX22029501,SRS19102284,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 4,R22,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R22,R22,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R22.fastq,fastq,23400.0,312.0,R22.fastq,0:75,A:7470;C:4460;G:5063;T:6404;N:3,75,,,,7470,4460,5063,6404,3,SRX22029501,SRS19102284,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87073,,0.12167,,0.99801,,0.73157,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28498,SRR26321414,SRX22029500,SRS19102281,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R21,R21,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R21,R21,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R21.fastq,fastq,23400.0,312.0,R21.fastq,0:75,A:7540;C:4349;G:4857;T:6646;N:8,75,,,,7540,4349,4857,6646,8,SRX22029500,SRS19102281,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.8839,,0.04494,,0.99768,,0.72769,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28499,SRR26321415,SRX22029499,SRS19102282,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 2,R18,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R18,R18,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R18.fastq,fastq,23400.0,312.0,R18.fastq,0:75,A:7380;C:4430;G:5069;T:6518;N:3,75,,,,7380,4430,5069,6518,3,SRX22029499,SRS19102282,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.11196,,0.99784,,0.69791,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28500,SRR26321416,SRX22029498,SRS19102280,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,1dpci 1,R17,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 1 dpci,R17,R17,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R17.fastq,fastq,23400.0,312.0,R17.fastq,0:75,A:7322;C:4455;G:5111;T:6507;N:5,75,,,,7322,4455,5111,6507,5,SRX22029498,SRS19102280,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90439,,0.12749,,0.99813,,0.71052,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28501,SRR26321417,SRX22029497,SRS19102279,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 5,R1,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R1,R1,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R1.fastq,fastq,23400.0,312.0,R1.fastq,0:75,A:7934;C:4560;G:4922;T:5980;N:4,75,,,,7934,4560,4922,5980,4,SRX22029497,SRS19102279,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87045,,0.10526,,0.99805,,0.71978,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28502,SRR26321418,SRX22029496,SRS19102277,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 4,R64,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R64,R64,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R64.fastq,fastq,23400.0,312.0,R64.fastq,0:75,A:7844;C:4626;G:4804;T:6126;N:0,75,,,,7844,4626,4804,6126,0,SRX22029496,SRS19102277,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90119,,0.07509,,0.99839,,0.8,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28503,SRR26321419,SRX22029495,SRS19102278,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 3,R61,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R61,R61,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R61.fastq,fastq,23400.0,312.0,R61.fastq,0:75,A:7454;C:4556;G:4960;T:6425;N:5,75,,,,7454,4556,4960,6425,5,SRX22029495,SRS19102278,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89098,,0.06015,,0.99813,,0.77102,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28504,SRR26321420,SRX22029494,SRS19102276,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 4,30,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,30,30,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,30.fastq,fastq,23400.0,312.0,30.fastq,0:75,A:7732;C:4528;G:5150;T:5987;N:3,75,,,,7732,4528,5150,5987,3,SRX22029494,SRS19102276,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.88447,,0.13147,,0.99772,,0.71584,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28505,SRR26321421,SRX22029493,SRS19102275,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,R11,R11,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R11,R11,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R11.fastq,fastq,23400.0,312.0,R11.fastq,0:75,A:7818;C:4507;G:5107;T:5956;N:12,75,,,,7818,4507,5107,5956,12,SRX22029493,SRS19102275,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.89345,,0.11475,,0.99847,,0.82258,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28506,SRR26321422,SRX22029492,SRS19102274,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 2,31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,31,31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,31.fastq,fastq,23400.0,312.0,31.fastq,0:75,A:7470;C:4619;G:4802;T:6504;N:5,75,,,,7470,4619,4802,6504,5,SRX22029492,SRS19102274,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87699,,0.11111,,0.99829,,0.78918,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28507,SRR26321423,SRX22029491,SRS19102273,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,7dpci 1,R9,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 7 dpci,R9,R9,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R9.fastq,fastq,23400.0,312.0,R9.fastq,0:75,A:8130;C:4537;G:4809;T:5917;N:7,75,,,,8130,4537,4809,5917,7,SRX22029491,SRS19102273,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.83588,,0.05725,,0.99801,,0.68586,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28508,SRR26321424,SRX22029490,SRS19102272,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 4,R33,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R33,R33,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R33.fastq,fastq,23400.0,312.0,R33.fastq,0:75,A:7745;C:4421;G:4867;T:6360;N:7,75,,,,7745,4421,4867,6360,7,SRX22029490,SRS19102272,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.87259,,0.07335,,0.99805,,0.71428,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28509,SRR26321425,SRX22029489,SRS19102271,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 3,R31,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R31,R31,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R31.fastq,fastq,23400.0,312.0,R31.fastq,0:75,A:7441;C:4483;G:5163;T:6313;N:0,75,,,,7441,4483,5163,6313,0,SRX22029489,SRS19102271,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.9,,0.05925,,0.9977,,0.68325,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28510,SRR26321426,SRX22029488,SRS19102270,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,3dpci 2,R29,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver 3 dpci,R29,R29,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R29.fastq,fastq,23400.0,312.0,R29.fastq,0:75,A:7379;C:4698;G:5166;T:6156;N:1,75,,,,7379,4698,5166,6156,1,SRX22029488,SRS19102270,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91016,,0.05859,,0.99797,,0.74528,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28511,SRR26321427,SRX22029487,SRS19102269,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,,SHAM 2,R62,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R62,R62,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R62.fastq,fastq,23400.0,312.0,R62.fastq,0:75,A:7383;C:4566;G:4713;T:6728;N:10,75,,,,7383,4566,4713,6728,10,SRX22029487,SRS19102269,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.91571,,0.05363,,0.99835,,0.77674,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
28512,SRR26321428,SRX22029486,SRS19102268,SRP465132,PRJNA1025903,Zebrafish cryoinjury regeneration Raw sequence reads,PRJNA1025903,Whole Genome Sequencing,Bulk RNA seq collection of adult zebrafish livers at different stages of regeneration upon liver croyinjury,,,Replicate 1 for SHAM,SHAM 1,R63,,strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:9 month|dev stage:maturity|collection date:2021 07 24|geo loc name:Australia: Melbourne|sex:male|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish liver sham,R63,R63,ham and injured livers at 1  3  and 7 dpci were phenotyped under the fluorescent stereomicroscope NSZ 606 Binocular Zoom fitted with a NightSea SFA light base to confirm the presence of insult upon cryoinjury. In addition  3 adult zebrafish livers were pooled per tube  discriminating between the injured border and liver tissue from other lobes. Finally  3 replicates of 3 pooled livers were used for library preparation. Livers were transferred to a final volume of 300uL of cold TRIzolTM Thermo Fisher Scientific per tube on ice. Livers were homogenized using the mechanical homogenizer for 30s on ice  with a plastic pestle  to ensure fine homogenization. RNA was extracted according to the manufacturer guidelines Direct zolTM RNA MiniPrep kit  Zymo Research. RNA quality was confirmed using an Agilent 4200 Tapestation System. Libraries were sequenced in Illumina NextSeq 500  with paired end 75bp reads to a depth of 15M reads per sample.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,NextSeq 500,,SRP465132,,,R63.fastq,fastq,23400.0,312.0,R63.fastq,0:75,A:7516;C:4606;G:4765;T:6508;N:5,75,,,,7516,4606,4765,6508,5,SRX22029486,SRS19102268,SRA1727674,Peter MacCallum Cancer Centre|Organogenesis and Cancer,Peter MacCallum Cancer Centre,1,0.90385,,0.0423,,0.99805,,0.72429,,75,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,unknown,bulk,bulk,bulk,,Australia,2023-10-11,Adult,Adult,Liver,Liver and Biliary System
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,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,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,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,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,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,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,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
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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
40043,SRR2751002,SRX1362072,SRS1125451,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 122,GSM1915508,,source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver,NH FLI liver 122,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,GSM1915508,GSM1915508: NH FLI liver 122; Danio rerio; RNA Seq,GSM1915508,,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:GSM1915508,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_12m_DR122.fq.gz,fastq,2275428550.0,45508571.0,GSM1915508 r1,0:50,A:594149425;C:543561508;G:537246828;T:600158700;N:312089,50,,,,594149425,543561508,537246828,600158700,312089,SRX1362072,SRS1125451,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.94529,,0.06272,,0.7722,,0.55271,,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
40044,SRR2751001,SRX1362071,SRS1125450,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 120,GSM1915507,,source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver,NH FLI liver 120,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,GSM1915507,GSM1915507: NH FLI liver 120; Danio rerio; RNA Seq,GSM1915507,,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:GSM1915507,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_12m_DR120.fq.gz,fastq,2265086750.0,45301735.0,GSM1915507 r1,0:50,A:601521692;C:533720206;G:522717695;T:606780756;N:346401,50,,,,601521692,533720206,522717695,606780756,346401,SRX1362071,SRS1125450,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93885,,0.08013,,0.76221,,0.58231,,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
40045,SRR2751000,SRX1362070,SRS1125452,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 98,GSM1915506,,source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver,NH FLI liver 98,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:6 month|age category:young|tissue:liver,GSM1915506,GSM1915506: NH FLI liver 98; Danio rerio; RNA Seq,GSM1915506,,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:GSM1915506,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_6m_DR98.fq.gz,fastq,2776070850.0,55521417.0,GSM1915506 r1,0:50,A:728235383;C:663729749;G:645210407;T:738761794;N:133517,50,,,,728235383,663729749,645210407,738761794,133517,SRX1362070,SRS1125452,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.94666,,0.05668,,0.82759,,0.56255,,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
40046,SRR2750999,SRX1362069,SRS1125453,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 96,GSM1915505,,source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver,NH FLI liver 96,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:6 month|age category:young|tissue:liver,GSM1915505,GSM1915505: NH FLI liver 96; Danio rerio; RNA Seq,GSM1915505,,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:GSM1915505,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_6m_DR96.fq.gz,fastq,2726829450.0,54536589.0,GSM1915505 r1,0:50,A:718243835;C:648108983;G:635655237;T:724565315;N:256080,50,,,,718243835,648108983,635655237,724565315,256080,SRX1362069,SRS1125453,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.94101,,0.06016,,0.81972,,0.5434,,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
40047,SRR2750998,SRX1362068,SRS1125458,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 86,GSM1915504,,source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver,NH FLI liver 86,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:6 month|age category:young|tissue:liver,GSM1915504,GSM1915504: NH FLI liver 86; Danio rerio; RNA Seq,GSM1915504,,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:GSM1915504,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_6m_DR86.fq.gz,fastq,2321789450.0,46435789.0,GSM1915504 r1,0:50,A:621943405;C:541049700;G:532136200;T:626281665;N:378480,50,,,,621943405,541049700,532136200,626281665,378480,SRX1362068,SRS1125458,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.94025,,0.08134,,0.76775,,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
40048,SRR2750997,SRX1362067,SRS1125454,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 85,GSM1915503,,source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver,NH FLI liver 85,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:6 month|age category:young|tissue:liver,GSM1915503,GSM1915503: NH FLI liver 85; Danio rerio; RNA Seq,GSM1915503,,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:GSM1915503,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP065208,,,liver_6m_DR85.fq.gz,fastq,2153807800.0,43076156.0,GSM1915503 r1,0:50,A:577891421;C:502278275;G:490571575;T:582818284;N:248245,50,,,,577891421,502278275,490571575,582818284,248245,SRX1362067,SRS1125454,SRA306458,GEO,Leibniz Institute for Age Research - Fritz Lipmann Institute,1,0.93585,,0.08978,,0.75365,,0.56334,,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
40709,SRR3420429,SRX1660365,SRS1360335,SRP072296,PRJNA316313,Codon optimality and mRNA decay in zebrafish and Xenopus,PRJNA316313,Other,Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved “codon optimality code” that shapes mRNA stability and translation efficiency across vertebrates.,,,,,AG01295 liver,,strain:TUAB|age:adult|sex:pooled male and female|tissue:Liver|BioSampleModel:Model organism or animal,,,,,,,,,AG01295 liver,AG01295 liver,1,1,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>75</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>,SRP072296,,,AG01295_SEQ0273_R1.fastq.gz,fastq,887443260.0,11676885.0,AG01295 run 1,0:76,A:230924609;C:202487813;G:205378868;T:248612177;N:39793,76,,,,230924609,202487813,205378868,248612177,39793,SRX1660365,SRS1360335,SRA395141,Yale University|Giraldez Lab,Yale University,1,0.95421,,0.04352,,0.84062,,0.23556,,76,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2016-06-17,Adult,Adult,Liver,Liver and Biliary System
40743,SRR3342393,SRX1684659,SRS1379870,SRP072957,PRJNA317597,FOXN3 regulates hepatic glucose utilization,GSE80003,Transcriptome Analysis,We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings,,pubmed:27292639,,Transgenic3,GSM2109873,,source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,Transgenic3,Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis,foxn3 overexpression liver,,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,,tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,GSM2109873,GSM2109873: Transgenic3; Danio rerio; RNA Seq,GSM2109873,,1,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,GEO Accession:GSM2109873,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP072957,,,11405X8_150225_D00294_0165_AC6BKMANXX_7.txt.gz,fastq,1538486450.0,30769729.0,GSM2109873 r1,0:50,A:399631224;C:339577730;G:345815787;T:453436273;N:25436,50,,,,399631224,339577730,345815787,453436273,25436,SRX1684659,SRS1379870,SRA405566,GEO,"Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine",1,0.89036,,0.28368,,0.75461,,0.63309,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-04-06,Larval,Larval,Liver,Liver and Biliary System
40744,SRR3342392,SRX1684658,SRS1379871,SRP072957,PRJNA317597,FOXN3 regulates hepatic glucose utilization,GSE80003,Transcriptome Analysis,We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings,,pubmed:27292639,,Transgenic2,GSM2109872,,source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,Transgenic2,Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis,foxn3 overexpression liver,,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,,tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,GSM2109872,GSM2109872: Transgenic2; Danio rerio; RNA Seq,GSM2109872,,1,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,GEO Accession:GSM2109872,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP072957,,,11405X7_150225_D00294_0165_AC6BKMANXX_7.txt.gz,fastq,1500971700.0,30019434.0,GSM2109872 r1,0:50,A:389353802;C:331408746;G:327481397;T:452703447;N:24308,50,,,,389353802,331408746,327481397,452703447,24308,SRX1684658,SRS1379871,SRA405566,GEO,"Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine",1,0.9148,,0.242,,0.76784,,0.44492,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-04-06,Larval,Larval,Liver,Liver and Biliary System
40745,SRR3342391,SRX1684657,SRS1379872,SRP072957,PRJNA317597,FOXN3 regulates hepatic glucose utilization,GSE80003,Transcriptome Analysis,We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings,,pubmed:27292639,,Transgenic1,GSM2109871,,source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,Transgenic1,Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis,foxn3 overexpression liver,,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,,tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae,GSM2109871,GSM2109871: Transgenic1; Danio rerio; RNA Seq,GSM2109871,,1,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,GEO Accession:GSM2109871,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP072957,,,11405X6_150225_D00294_0165_AC6BKMANXX_7.txt.gz,fastq,1672645200.0,33452904.0,GSM2109871 r1,0:50,A:446934700;C:363616773;G:354194568;T:507871249;N:27910,50,,,,446934700,363616773,354194568,507871249,27910,SRX1684657,SRS1379872,SRA405566,GEO,"Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine",1,0.90431,,0.33357,,0.75075,,0.62394,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-04-06,Larval,Larval,Liver,Liver and Biliary System
40746,SRR3342390,SRX1684656,SRS1379873,SRP072957,PRJNA317597,FOXN3 regulates hepatic glucose utilization,GSE80003,Transcriptome Analysis,We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings,,pubmed:27292639,,WT3,GSM2109870,,source name:wildtype liver|tissue:Liver|developmental stage:7 dpf larvae,WT3,Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis,wildtype liver,,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,,tissue:Liver|developmental stage:7 dpf larvae,GSM2109870,GSM2109870: WT3; Danio rerio; RNA Seq,GSM2109870,,1,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,GEO Accession:GSM2109870,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP072957,,,11405X4_150225_D00294_0165_AC6BKMANXX_7.txt.gz,fastq,1621245550.0,32424911.0,GSM2109870 r1,0:50,A:387275594;C:392477306;G:410916447;T:430550072;N:26131,50,,,,387275594,392477306,410916447,430550072,26131,SRX1684656,SRS1379873,SRA405566,GEO,"Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine",1,0.75787,,0.22112,,0.80858,,0.6379,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-04-06,Larval,Larval,Liver,Liver and Biliary System
40747,SRR3342389,SRX1684655,SRS1379874,SRP072957,PRJNA317597,FOXN3 regulates hepatic glucose utilization,GSE80003,Transcriptome Analysis,We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings,,pubmed:27292639,,WT2,GSM2109869,,source name:wildtype liver|tissue:Liver|developmental stage:7 dpf larvae,WT2,Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis,wildtype liver,,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,,tissue:Liver|developmental stage:7 dpf larvae,GSM2109869,GSM2109869: WT2; Danio rerio; RNA Seq,GSM2109869,,1,Total RNA  extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine,GEO Accession:GSM2109869,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP072957,,,11405X3_150225_D00294_0165_AC6BKMANXX_7.txt.gz,fastq,1660295850.0,33205917.0,GSM2109869 r1,0:50,A:441731711;C:362842137;G:351944677;T:503749546;N:27779,50,,,,441731711,362842137,351944677,503749546,27779,SRX1684655,SRS1379874,SRA405566,GEO,"Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine",1,0.90993,,0.31148,,0.74602,,0.62587,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-04-06,Larval,Larval,Liver,Liver and Biliary System