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
48021,SRR6915090,SRX3862779,SRS3104834,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate3,GSM3071386,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071386,GSM3071386: 10dpa replicate3; Danio rerio; RNA Seq,GSM3071386,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071386,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_10-10.bam,bam,682375516.0,14088728.0,GSM3071386 r1,0:48.43,A:140419665;C:148759068;G:176799261;T:168695522;N:47702000,48,,,,140419665,148759068,176799261,168695522,47702000,SRX3862779,SRS3104834,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.76603,,0.04459,,0.79752,,0.50424,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48022,SRR6915089,SRX3862778,SRS3104833,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate3,GSM3071385,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071385,GSM3071385: 3dpa replicate3; Danio rerio; RNA Seq,GSM3071385,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071385,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_12-12.bam,bam,901887293.0,18522789.0,GSM3071385 r1,0:48.69,A:184300673;C:193849264;G:243428119;T:224471972;N:55837265,48,,,,184300673,193849264,243428119,224471972,55837265,SRX3862778,SRS3104833,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.78632,,0.03154,,0.79707,,0.51779,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48023,SRR6915088,SRX3862777,SRS3104832,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate3,GSM3071384,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071384,GSM3071384: 2dpa replicate3; Danio rerio; RNA Seq,GSM3071384,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071384,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_11-11.bam,bam,850810410.0,17462158.0,GSM3071384 r1,0:48.72,A:176186499;C:182052044;G:228063922;T:213571294;N:50936651,48,,,,176186499,182052044,228063922,213571294,50936651,SRX3862777,SRS3104832,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.77804,,0.03462,,0.80229,,0.49822,,43,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48024,SRR6915087,SRX3862776,SRS3104831,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate3,GSM3071383,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate3,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071383,GSM3071383: 0dpa replicate3; Danio rerio; RNA Seq,GSM3071383,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071383,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L03-1-Idx_9-9.bam,bam,598710241.0,12328728.0,GSM3071383 r1,0:48.56,A:121889198;C:129444719;G:158430979;T:150128070;N:38817275,48,,,,121889198,129444719,158430979,150128070,38817275,SRX3862776,SRS3104831,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.77,,0.03334,,0.799,,0.45925,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48025,SRR6915086,SRX3862775,SRS3104830,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate2,GSM3071382,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071382,GSM3071382: 10dpa replicate2; Danio rerio; RNA Seq,GSM3071382,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071382,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_8-8.bam,bam,1205021238.0,24639106.0,GSM3071382 r1,0:48.91,A:255022070;C:275793907;G:309172527;T:294800027;N:70232707,48,,,,255022070,275793907,309172527,294800027,70232707,SRX3862775,SRS3104830,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80398,,0.05829,,0.78644,,0.4993,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48026,SRR6915085,SRX3862774,SRS3104829,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate2,GSM3071381,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071381,GSM3071381: 3dpa replicate2; Danio rerio; RNA Seq,GSM3071381,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071381,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_10-10.bam,bam,1479531813.0,30219937.0,GSM3071381 r1,0:48.96,A:314793261;C:331769330;G:384109921;T:369987947;N:78871354,48,,,,314793261,331769330,384109921,369987947,78871354,SRX3862774,SRS3104829,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81777,,0.03195,,0.7821,,0.49263,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48027,SRR6915084,SRX3862773,SRS3104828,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate2,GSM3071380,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071380,GSM3071380: 2dpa replicate2; Danio rerio; RNA Seq,GSM3071380,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071380,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_9-9.bam,bam,834856811.0,17079585.0,GSM3071380 r1,0:48.88,A:179851654;C:186667201;G:209784080;T:212166083;N:46387793,48,,,,179851654,186667201,209784080,212166083,46387793,SRX3862773,SRS3104828,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80341,,0.02786,,0.78031,,0.49876,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48028,SRR6915083,SRX3862772,SRS3104827,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate2,GSM3071379,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate2,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071379,GSM3071379: 0dpa replicate2; Danio rerio; RNA Seq,GSM3071379,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071379,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L02-1-Idx_7-7.bam,bam,821645371.0,16824250.0,GSM3071379 r1,0:48.84,A:169383232;C:176200663;G:223364159;T:207905438;N:44791879,48,,,,169383232,176200663,223364159,207905438,44791879,SRX3862772,SRS3104827,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.79697,,0.04152,,0.79513,,0.48078,,34,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48029,SRR6915082,SRX3862771,SRS3104826,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,10dpa replicate1,GSM3071378,,source name:caudal fin tissue 10 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,10dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 10 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071378,GSM3071378: 10dpa replicate1; Danio rerio; RNA Seq,GSM3071378,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071378,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_4-4.bam,bam,1056921416.0,21553661.0,GSM3071378 r1,0:49.04,A:223138065;C:233998717;G:286278215;T:261736901;N:51769518,49,,,,223138065,233998717,286278215,261736901,51769518,SRX3862771,SRS3104826,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81372,,0.06015,,0.79017,,0.49818,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48030,SRR6915081,SRX3862770,SRS3104824,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,3dpa replicate1,GSM3071377,,source name:caudal fin tissue 3 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,3dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 3 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071377,GSM3071377: 3dpa replicate1; Danio rerio; RNA Seq,GSM3071377,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071377,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_6-6.bam,bam,614372216.0,12531168.0,GSM3071377 r1,0:49.03,A:129828689;C:133826356;G:168985348;T:153858339;N:27873484,49,,,,129828689,133826356,168985348,153858339,27873484,SRX3862770,SRS3104824,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81659,,0.02803,,0.78987,,0.49295,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48031,SRR6915080,SRX3862769,SRS3104825,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,2dpa replicate1,GSM3071376,,source name:caudal fin tissue 2 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,2dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 2 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071376,GSM3071376: 2dpa replicate1; Danio rerio; RNA Seq,GSM3071376,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071376,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_5-5.bam,bam,1317408760.0,26870813.0,GSM3071376 r1,0:49.03,A:278980295;C:285236037;G:357022664;T:334390621;N:61779143,49,,,,278980295,285236037,357022664,334390621,61779143,SRX3862769,SRS3104825,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.81546,,0.02559,,0.79328,,0.48857,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure
48032,SRR6915079,SRX3862768,SRS3104823,SRP136710,PRJNA447984,RNA seq data from adult zebrafish caudal fin regeneration,GSE112498,Transcriptome Analysis,Adult zebrafish are able to regenerate many organs such as their caudal fin in only few dy post amputation. To explore the landscape and dynamic of the genes involed in regeneration  we performed a global transcriptomic analysis using RNA seq during zebrafish caudal fin regeneration. Overall design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2  3 and 10 dy post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.,,pubmed:30031067,,0dpa replicate1,GSM3071375,,source name:caudal fin tissue 0 dy post amputation|tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,0dpa replicate1,SOLiD Wildfire sequencer Thermo Fisher Scientific Mapping was performed in color space using the dedicated Lifescope pipeline and the whole.transcriptome.frag workflow Genome build: zv9 Supplementary files format and content: Data raw counts are provided as a table where each line corresponds to a gene and each column to a sample,caudal fin tissue 0 dy post amputation,Samples were collected on anesthetized fish and washed one time in water. Samples were then placed in the Macherey Nagel RNA XS kit ref. 740902 lysis buffer and stored at  80°C before RNA extraction.,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,Adult fish were raised at 28°C and fed 2 times a day. Fish were anesthetized for the first fin amputation and then at appropriate time points to take off samples.,tissue:caudal fin|strain:AB Tu|age:adults between 8 mpf and 18 mpf,GSM3071375,GSM3071375: 0dpa replicate1; Danio rerio; RNA Seq,GSM3071375,,1,RNAs were extracted using the Macherey Nagel RNA XS kit ref. 740902 and according to manufacturer's instructions exept that the carrier RNA was not used. Libraries were built using the SENSE mRNA Seq Library Prep Kit Lexogen dedicated for SOLiD sequencers. Librairies were then converted to 5500W system to be compatible with the SOLiD Wildfire sequencer.,GEO Accession:GSM3071375,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB 5500 Genetic Analyzer,,SRP136710,,options:  accept hard clip,Solid5500_2014_11_07_1_L01-1-Idx_3-3.bam,bam,975324708.0,19881338.0,GSM3071375 r1,0:49.06,A:203549346;C:215407985;G:265949502;T:244027187;N:46390688,49,,,,203549346,215407985,265949502,244027187,46390688,SRX3862768,SRS3104823,SRA676352,GEO,"Matrix Biology and Pathology group, Institute of Functional Genomics of Lyon, CNRS - ENS of Lyon",1,0.80817,,0.05047,,0.79569,,0.47149,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,lexogen,bulk,unknown,unknown,,France,2018-03-29,Adult,Adult,Fin,Surface Structure